chore(restructure): add .git-blame-ignore-revs for restructure commits

Tells git blame (and GitHub) to skip the git-mv and import-rewrite
commits so blame shows the original author.

.git-blame-ignore-revs

@@ -0,0 +1,5 @@
+# hermes_agent package restructure (PR 1/3)
+# Commit 2: pure git mv — all source files into hermes_agent/
+65ca3ba93b3fa7fd2b15af5b62d54020061f3672
+# Commit 3: rewrite all imports for hermes_agent package
+4b16341975a1217588054f567d0f76dc5a3cc481

AGENTS.md

@@ -12,68 +12,59 @@ source venv/bin/activate  # ALWAYS activate before running Python
 
 ```
 hermes-agent/
-├── run_agent.py          # AIAgent class — core conversation loop
-├── model_tools.py        # Tool orchestration, discover_builtin_tools(), handle_function_call()
-├── toolsets.py           # Toolset definitions, _HERMES_CORE_TOOLS list
-├── cli.py                # HermesCLI class — interactive CLI orchestrator
-├── hermes_state.py       # SessionDB — SQLite session store (FTS5 search)
-├── agent/                # Agent internals
-│   ├── prompt_builder.py     # System prompt assembly
-│   ├── context_compressor.py # Auto context compression
-│   ├── prompt_caching.py     # Anthropic prompt caching
-│   ├── auxiliary_client.py   # Auxiliary LLM client (vision, summarization)
-│   ├── model_metadata.py     # Model context lengths, token estimation
-│   ├── models_dev.py         # models.dev registry integration (provider-aware context)
-│   ├── display.py            # KawaiiSpinner, tool preview formatting
-│   ├── skill_commands.py     # Skill slash commands (shared CLI/gateway)
-│   └── trajectory.py         # Trajectory saving helpers
-├── hermes_cli/           # CLI subcommands and setup
-│   ├── main.py           # Entry point — all `hermes` subcommands
-│   ├── config.py         # DEFAULT_CONFIG, OPTIONAL_ENV_VARS, migration
-│   ├── commands.py       # Slash command definitions + SlashCommandCompleter
-│   ├── callbacks.py      # Terminal callbacks (clarify, sudo, approval)
-│   ├── setup.py          # Interactive setup wizard
-│   ├── skin_engine.py    # Skin/theme engine — CLI visual customization
-│   ├── skills_config.py  # `hermes skills` — enable/disable skills per platform
-│   ├── tools_config.py   # `hermes tools` — enable/disable tools per platform
-│   ├── skills_hub.py     # `/skills` slash command (search, browse, install)
-│   ├── models.py         # Model catalog, provider model lists
-│   ├── model_switch.py   # Shared /model switch pipeline (CLI + gateway)
-│   └── auth.py           # Provider credential resolution
-├── tools/                # Tool implementations (one file per tool)
-│   ├── registry.py       # Central tool registry (schemas, handlers, dispatch)
-│   ├── approval.py       # Dangerous command detection
-│   ├── terminal_tool.py  # Terminal orchestration
-│   ├── process_registry.py # Background process management
-│   ├── file_tools.py     # File read/write/search/patch
-│   ├── web_tools.py      # Web search/extract (Parallel + Firecrawl)
-│   ├── browser_tool.py   # Browserbase browser automation
-│   ├── code_execution_tool.py # execute_code sandbox
-│   ├── delegate_tool.py  # Subagent delegation
-│   ├── mcp_tool.py       # MCP client (~1050 lines)
-│   └── environments/     # Terminal backends (local, docker, ssh, modal, daytona, singularity)
-├── gateway/              # Messaging platform gateway
-│   ├── run.py            # Main loop, slash commands, message dispatch
-│   ├── session.py        # SessionStore — conversation persistence
-│   └── platforms/        # Adapters: telegram, discord, slack, whatsapp, homeassistant, signal, qqbot
-├── ui-tui/               # Ink (React) terminal UI — `hermes --tui`
-│   ├── src/entry.tsx        # TTY gate + render()
-│   ├── src/app.tsx          # Main state machine and UI
-│   ├── src/gatewayClient.ts # Child process + JSON-RPC bridge
-│   ├── src/app/             # Decomposed app logic (event handler, slash handler, stores, hooks)
-│   ├── src/components/      # Ink components (branding, markdown, prompts, pickers, etc.)
-│   ├── src/hooks/           # useCompletion, useInputHistory, useQueue, useVirtualHistory
-│   └── src/lib/             # Pure helpers (history, osc52, text, rpc, messages)
+├── hermes_agent/             # Single installable package
+│   ├── agent/                # Core conversation loop and agent internals
+│   │   ├── loop.py               # AIAgent class — core conversation loop
+│   │   ├── prompt_builder.py     # System prompt assembly
+│   │   ├── context/              # Context management (engine, compressor, references)
+│   │   ├── memory/               # Memory management (manager, provider)
+│   │   ├── image_gen/            # Image generation (provider, registry)
+│   │   ├── display.py            # KawaiiSpinner, tool preview formatting
+│   │   ├── skill_commands.py     # Skill slash commands (shared CLI/gateway)
+│   │   └── trajectory.py         # Trajectory saving helpers
+│   ├── providers/            # LLM provider adapters and transports
+│   │   ├── anthropic_adapter.py  # Anthropic adapter
+│   │   ├── anthropic_transport.py # Anthropic transport
+│   │   ├── metadata.py           # Model context lengths, token estimation
+│   │   ├── auxiliary.py           # Auxiliary LLM client (vision, summarization)
+│   │   ├── caching.py            # Anthropic prompt caching
+│   │   └── credential_pool.py    # Credential management
+│   ├── tools/                # Tool implementations
+│   │   ├── dispatch.py           # Tool orchestration, discover_builtin_tools()
+│   │   ├── toolsets.py           # Toolset definitions
+│   │   ├── registry.py           # Central tool registry
+│   │   ├── terminal.py           # Terminal orchestration
+│   │   ├── browser/              # Browser tools (tool, cdp, camofox, providers/)
+│   │   ├── mcp/                  # MCP client and server
+│   │   ├── skills/               # Skill management (manager, tool, hub, guard, sync)
+│   │   ├── media/                # Voice, TTS, transcription, image gen
+│   │   ├── files/                # File operations (tools, operations, state)
+│   │   └── security/             # Path security, URL safety, approval
+│   ├── backends/             # Terminal backends (local, docker, ssh, modal, daytona, singularity)
+│   ├── cli/                  # CLI subcommands and setup
+│   │   ├── main.py               # Entry point — all `hermes` subcommands
+│   │   ├── repl.py               # HermesCLI class — interactive CLI orchestrator
+│   │   ├── config.py             # DEFAULT_CONFIG, OPTIONAL_ENV_VARS, migration
+│   │   ├── commands.py           # Slash command definitions
+│   │   ├── auth/                 # Provider credential resolution
+│   │   ├── models/               # Model catalog, provider lists, switching
+│   │   └── ui/                   # Banner, colors, skin engine, callbacks, tips
+│   ├── gateway/              # Messaging platform gateway
+│   │   ├── run.py                # Main loop, slash commands, message dispatch
+│   │   ├── session.py            # SessionStore — conversation persistence
+│   │   └── platforms/            # Adapters: telegram, discord, slack, whatsapp, etc.
+│   ├── acp/                  # ACP server (VS Code / Zed / JetBrains integration)
+│   ├── cron/                 # Scheduler (jobs.py, scheduler.py)
+│   ├── plugins/              # Plugin system (memory providers, context engines)
+│   ├── constants.py          # Shared constants
+│   ├── state.py              # SessionDB — SQLite session store
+│   ├── logging.py            # Logging configuration
+│   └── utils.py              # Shared utilities
 ├── tui_gateway/          # Python JSON-RPC backend for the TUI
-│   ├── entry.py             # stdio entrypoint
-│   ├── server.py            # RPC handlers and session logic
-│   ├── render.py            # Optional rich/ANSI bridge
-│   └── slash_worker.py      # Persistent HermesCLI subprocess for slash commands
-├── acp_adapter/          # ACP server (VS Code / Zed / JetBrains integration)
-├── cron/                 # Scheduler (jobs.py, scheduler.py)
+├── ui-tui/               # Ink (React) terminal UI — `hermes --tui`
 ├── environments/         # RL training environments (Atropos)
-├── tests/                # Pytest suite (~3000 tests)
-└── batch_runner.py       # Parallel batch processing
+├── tests/                # Pytest suite
+└── web/                  # Vite + React web dashboard
 ```
 
 **User config:** `~/.hermes/config.yaml` (settings), `~/.hermes/.env` (API keys)
@@ -81,18 +72,18 @@ hermes-agent/
 ## File Dependency Chain
 
 ```
-tools/registry.py  (no deps — imported by all tool files)
+hermes_agent/tools/registry.py  (no deps — imported by all tool files)
        ↑
-tools/*.py  (each calls registry.register() at import time)
+hermes_agent/tools/*.py  (each calls registry.register() at import time)
        ↑
-model_tools.py  (imports tools/registry + triggers tool discovery)
+hermes_agent/tools/dispatch.py  (imports registry + triggers tool discovery)
        ↑
-run_agent.py, cli.py, batch_runner.py, environments/
+hermes_agent/agent/loop.py, hermes_agent/cli/repl.py, environments/
 ```
 
 ---
 
-## AIAgent Class (run_agent.py)
+## AIAgent Class (hermes_agent/agent/loop.py)
 
 ```python
 class AIAgent:
@@ -138,14 +129,14 @@ Messages follow OpenAI format: `{"role": "system/user/assistant/tool", ...}`. Re
 
 ---
 
-## CLI Architecture (cli.py)
+## CLI Architecture (hermes_agent/cli/repl.py)
 
 - **Rich** for banner/panels, **prompt_toolkit** for input with autocomplete
-- **KawaiiSpinner** (`agent/display.py`) — animated faces during API calls, `┊` activity feed for tool results
-- `load_cli_config()` in cli.py merges hardcoded defaults + user config YAML
-- **Skin engine** (`hermes_cli/skin_engine.py`) — data-driven CLI theming; initialized from `display.skin` config key at startup; skins customize banner colors, spinner faces/verbs/wings, tool prefix, response box, branding text
+- **KawaiiSpinner** (`hermes_agent/agent/display.py`) — animated faces during API calls, `┊` activity feed for tool results
+- `load_cli_config()` in repl.py merges hardcoded defaults + user config YAML
+- **Skin engine** (`hermes_agent/cli/ui/skin_engine.py`) — data-driven CLI theming; initialized from `display.skin` config key at startup; skins customize banner colors, spinner faces/verbs/wings, tool prefix, response box, branding text
 - `process_command()` is a method on `HermesCLI` — dispatches on canonical command name resolved via `resolve_command()` from the central registry
-- Skill slash commands: `agent/skill_commands.py` scans `~/.hermes/skills/`, injects as **user message** (not system prompt) to preserve prompt caching
+- Skill slash commands: `hermes_agent/agent/skill_commands.py` scans `~/.hermes/skills/`, injects as **user message** (not system prompt) to preserve prompt caching
 
 ### Slash Command Registry (`hermes_cli/commands.py`)
 
@@ -272,7 +263,7 @@ registry.register(
 
 **2. Add to `toolsets.py`** — either `_HERMES_CORE_TOOLS` (all platforms) or a new toolset.
 
-Auto-discovery: any `tools/*.py` file with a top-level `registry.register()` call is imported automatically — no manual import list to maintain.
+Auto-discovery: any `hermes_agent/tools/*.py` file with a top-level `registry.register()` call is imported automatically — no manual import list to maintain.
 
 The registry handles schema collection, dispatch, availability checking, and error wrapping. All handlers MUST return a JSON string.
 
@@ -498,11 +489,11 @@ Rendering bugs in tmux/iTerm2 — ghosting on scroll. Use `curses` (stdlib) inst
 ### DO NOT use `\033[K` (ANSI erase-to-EOL) in spinner/display code
 Leaks as literal `?[K` text under `prompt_toolkit`'s `patch_stdout`. Use space-padding: `f"\r{line}{' ' * pad}"`.
 
-### `_last_resolved_tool_names` is a process-global in `model_tools.py`
+### `_last_resolved_tool_names` is a process-global in `hermes_agent/tools/dispatch.py`
 `_run_single_child()` in `delegate_tool.py` saves and restores this global around subagent execution. If you add new code that reads this global, be aware it may be temporarily stale during child agent runs.
 
 ### DO NOT hardcode cross-tool references in schema descriptions
-Tool schema descriptions must not mention tools from other toolsets by name (e.g., `browser_navigate` saying "prefer web_search"). Those tools may be unavailable (missing API keys, disabled toolset), causing the model to hallucinate calls to non-existent tools. If a cross-reference is needed, add it dynamically in `get_tool_definitions()` in `model_tools.py` — see the `browser_navigate` / `execute_code` post-processing blocks for the pattern.
+Tool schema descriptions must not mention tools from other toolsets by name (e.g., `browser_navigate` saying "prefer web_search"). Those tools may be unavailable (missing API keys, disabled toolset), causing the model to hallucinate calls to non-existent tools. If a cross-reference is needed, add it dynamically in `get_tool_definitions()` in `hermes_agent/tools/dispatch.py` — see the `browser_navigate` / `execute_code` post-processing blocks for the pattern.
 
 ### Tests must not write to `~/.hermes/`
 The `_isolate_hermes_home` autouse fixture in `tests/conftest.py` redirects `HERMES_HOME` to a temp dir. Never hardcode `~/.hermes/` paths in tests.

Dockerfile

@@ -38,7 +38,7 @@ RUN npm install --prefer-offline --no-audit && \
 # .dockerignore excludes node_modules, so the installs above survive.
 COPY --chown=hermes:hermes . .
 
-# Build web dashboard (Vite outputs to hermes_cli/web_dist/)
+# Build web dashboard (Vite outputs to hermes_agent/cli/web_dist/)
 RUN cd web && npm run build
 
 # ---------- Python virtualenv ----------
@@ -48,7 +48,7 @@ RUN uv venv && \
     uv pip install --no-cache-dir -e ".[all]"
 
 # ---------- Runtime ----------
-ENV HERMES_WEB_DIST=/opt/hermes/hermes_cli/web_dist
+ENV HERMES_WEB_DIST=/opt/hermes/hermes_agent/cli/web_dist
 ENV HERMES_HOME=/opt/data
 VOLUME [ "/opt/data" ]
 ENTRYPOINT [ "/opt/hermes/docker/entrypoint.sh" ]

MANIFEST.in

@@ -1,3 +1,4 @@
+graft hermes_agent
 graft skills
 graft optional-skills
 global-exclude __pycache__

datagen-config-examples/run_browser_tasks.sh

@@ -29,7 +29,7 @@ echo "📝 Logging to: $LOG_FILE"
 # Point to the example dataset in this directory
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 
-python batch_runner.py \
+python scripts/batch_runner.py \
   --dataset_file="$SCRIPT_DIR/example_browser_tasks.jsonl" \
   --batch_size=5 \
   --run_name="browser_tasks_example" \

datagen-config-examples/web_research.yaml

@@ -4,7 +4,7 @@
 # Generates tool-calling trajectories for multi-step web research tasks.
 #
 # Usage:
-#   python batch_runner.py \
+#   python scripts/batch_runner.py \
 #     --config datagen-config-examples/web_research.yaml \
 #     --run_name web_research_v1
 

docker/entrypoint.sh

@@ -65,7 +65,7 @@ fi
 
 # Sync bundled skills (manifest-based so user edits are preserved)
 if [ -d "$INSTALL_DIR/skills" ]; then
-    python3 "$INSTALL_DIR/tools/skills_sync.py"
+    hermes-skills-sync
 fi
 
 exec hermes "$@"

environments/agent_loop.py

@@ -18,11 +18,14 @@ import logging
 import os
 import uuid
 from dataclasses import dataclass, field
-from typing import Any, Dict, List, Optional, Set
+from typing import Any, Dict, List, Optional, Set, TYPE_CHECKING
 
-from model_tools import handle_function_call
-from tools.terminal_tool import get_active_env
-from tools.tool_result_storage import maybe_persist_tool_result, enforce_turn_budget
+if TYPE_CHECKING:
+    from hermes_agent.tools.budget_config import BudgetConfig
+
+from hermes_agent.tools.dispatch import handle_function_call
+from hermes_agent.tools.terminal import get_active_env
+from hermes_agent.tools.result_storage import maybe_persist_tool_result, enforce_turn_budget
 
 # Thread pool for running sync tool calls that internally use asyncio.run()
 # (e.g., the Modal/Docker/Daytona terminal backends). Running them in a separate
@@ -161,7 +164,7 @@ class HermesAgentLoop:
                         thresholds, per-turn aggregate budget, and preview size.
                         If None, uses DEFAULT_BUDGET (current hardcoded values).
         """
-        from tools.budget_config import DEFAULT_BUDGET
+        from hermes_agent.tools.budget_config import DEFAULT_BUDGET
         self.server = server
         self.tool_schemas = tool_schemas
         self.valid_tool_names = valid_tool_names
@@ -187,7 +190,7 @@ class HermesAgentLoop:
         tool_errors: List[ToolError] = []
 
         # Per-loop TodoStore for the todo tool (ephemeral, dies with the loop)
-        from tools.todo_tool import TodoStore, todo_tool as _todo_tool
+        from hermes_agent.tools.todo import TodoStore, todo_tool as _todo_tool
         _todo_store = TodoStore()
 
         # Extract user task from first user message for browser_snapshot context

environments/benchmarks/terminalbench_2/terminalbench2_env.py

@@ -60,7 +60,7 @@ from atroposlib.envs.server_handling.server_manager import APIServerConfig
 from environments.agent_loop import AgentResult, HermesAgentLoop
 from environments.hermes_base_env import HermesAgentBaseEnv, HermesAgentEnvConfig
 from environments.tool_context import ToolContext
-from tools.terminal_tool import (
+from hermes_agent.tools.terminal import (
     register_task_env_overrides,
     clear_task_env_overrides,
     cleanup_vm,
@@ -876,7 +876,7 @@ class TerminalBench2EvalEnv(HermesAgentBaseEnv):
             # Let cancellations propagate (finally blocks run cleanup_vm)
             await asyncio.gather(*eval_tasks, return_exceptions=True)
             # Belt-and-suspenders: clean up any remaining sandboxes
-            from tools.terminal_tool import cleanup_all_environments
+            from hermes_agent.tools.terminal import cleanup_all_environments
             cleanup_all_environments()
             print("All sandboxes cleaned up.")
             return
@@ -984,7 +984,7 @@ class TerminalBench2EvalEnv(HermesAgentBaseEnv):
 
         # Kill all remaining sandboxes. Timed-out tasks leave orphaned thread
         # pool workers still executing commands -- cleanup_all stops them.
-        from tools.terminal_tool import cleanup_all_environments
+        from hermes_agent.tools.terminal import cleanup_all_environments
         print("\nCleaning up all sandboxes...")
         cleanup_all_environments()
 

environments/benchmarks/yc_bench/yc_bench_env.py

@@ -709,7 +709,7 @@ class YCBenchEvalEnv(HermesAgentBaseEnv):
             tqdm.write("\n[INTERRUPTED] Stopping evaluation...")
             pbar.close()
             try:
-                from tools.terminal_tool import cleanup_all_environments
+                from hermes_agent.tools.terminal import cleanup_all_environments
                 cleanup_all_environments()
             except Exception:
                 pass
@@ -819,7 +819,7 @@ class YCBenchEvalEnv(HermesAgentBaseEnv):
             print(f"Results saved to: {self._streaming_path}")
 
         try:
-            from tools.terminal_tool import cleanup_all_environments
+            from hermes_agent.tools.terminal import cleanup_all_environments
             cleanup_all_environments()
         except Exception:
             pass

environments/hermes_base_env.py

@@ -62,15 +62,15 @@ from atroposlib.type_definitions import Item
 
 from environments.agent_loop import AgentResult, HermesAgentLoop
 from environments.tool_context import ToolContext
-from tools.budget_config import (
+from hermes_agent.tools.budget_config import (
     DEFAULT_RESULT_SIZE_CHARS,
     DEFAULT_TURN_BUDGET_CHARS,
     DEFAULT_PREVIEW_SIZE_CHARS,
 )
 
 # Import hermes-agent toolset infrastructure
-from model_tools import get_tool_definitions
-from toolset_distributions import sample_toolsets_from_distribution
+from hermes_agent.tools.dispatch import get_tool_definitions
+from hermes_agent.tools.distributions import sample_toolsets_from_distribution
 
 logger = logging.getLogger(__name__)
 
@@ -209,7 +209,7 @@ class HermesAgentEnvConfig(BaseEnvConfig):
 
     def build_budget_config(self):
         """Build a BudgetConfig from env config fields."""
-        from tools.budget_config import BudgetConfig
+        from hermes_agent.tools.budget_config import BudgetConfig
         return BudgetConfig(
             default_result_size=self.default_result_size_chars,
             turn_budget=self.turn_budget_chars,

environments/tool_context.py

@@ -31,9 +31,9 @@ from typing import Any, Dict, List, Optional
 import asyncio
 import concurrent.futures
 
-from model_tools import handle_function_call
-from tools.terminal_tool import cleanup_vm
-from tools.browser_tool import cleanup_browser
+from hermes_agent.tools.dispatch import handle_function_call
+from hermes_agent.tools.terminal import cleanup_vm
+from hermes_agent.tools.browser.tool import cleanup_browser
 
 logger = logging.getLogger(__name__)
 
@@ -446,7 +446,7 @@ class ToolContext:
         """
         # Kill any background processes from this rollout (safety net)
         try:
-            from tools.process_registry import process_registry
+            from hermes_agent.tools.process_registry import process_registry
             killed = process_registry.kill_all(task_id=self.task_id)
             if killed:
                 logger.debug("Process cleanup for task %s: killed %d process(es)", self.task_id, killed)

hermes

@@ -7,5 +7,5 @@ subcommands such as `gateway`, `cron`, and `doctor`.
 """
 
 if __name__ == "__main__":
-    from hermes_cli.main import main
+    from hermes_agent.cli.main import main
     main()

hermes_agent/acp/auth.py

@@ -8,7 +8,7 @@ from typing import Optional
 def detect_provider() -> Optional[str]:
     """Resolve the active Hermes runtime provider, or None if unavailable."""
     try:
-        from hermes_cli.runtime_provider import resolve_runtime_provider
+        from hermes_agent.cli.runtime_provider import resolve_runtime_provider
         runtime = resolve_runtime_provider()
         api_key = runtime.get("api_key")
         provider = runtime.get("provider")

hermes_agent/acp/entry.py

@@ -17,7 +17,7 @@ import asyncio
 import logging
 import sys
 from pathlib import Path
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 
 # Methods clients send as periodic liveness probes. They are not part of the
@@ -83,7 +83,7 @@ def _setup_logging() -> None:
 
 def _load_env() -> None:
     """Load .env from HERMES_HOME (default ``~/.hermes``)."""
-    from hermes_cli.env_loader import load_hermes_dotenv
+    from hermes_agent.cli.env_loader import load_hermes_dotenv
 
     hermes_home = get_hermes_home()
     loaded = load_hermes_dotenv(hermes_home=hermes_home)
@@ -104,11 +104,6 @@ def main() -> None:
     logger = logging.getLogger(__name__)
     logger.info("Starting hermes-agent ACP adapter")
 
-    # Ensure the project root is on sys.path so ``from run_agent import AIAgent`` works
-    project_root = str(Path(__file__).resolve().parent.parent)
-    if project_root not in sys.path:
-        sys.path.insert(0, project_root)
-
     import acp
     from .server import HermesACPAgent
 

hermes_agent/acp/events.py

@@ -88,7 +88,7 @@ def make_tool_progress_cb(
         snapshot = None
         if name in {"write_file", "patch", "skill_manage"}:
             try:
-                from agent.display import capture_local_edit_snapshot
+                from hermes_agent.agent.display import capture_local_edit_snapshot
 
                 snapshot = capture_local_edit_snapshot(name, args)
             except Exception:

hermes_agent/acp/server.py

@@ -52,20 +52,20 @@ try:
 except ImportError:
     from acp.schema import AuthMethod as AuthMethodAgent  # type: ignore[attr-defined]
 
-from acp_adapter.auth import detect_provider
-from acp_adapter.events import (
+from hermes_agent.acp.auth import detect_provider
+from hermes_agent.acp.events import (
     make_message_cb,
     make_step_cb,
     make_thinking_cb,
     make_tool_progress_cb,
 )
-from acp_adapter.permissions import make_approval_callback
-from acp_adapter.session import SessionManager, SessionState
+from hermes_agent.acp.permissions import make_approval_callback
+from hermes_agent.acp.session import SessionManager, SessionState
 
 logger = logging.getLogger(__name__)
 
 try:
-    from hermes_cli import __version__ as HERMES_VERSION
+    from hermes_agent.cli import __version__ as HERMES_VERSION
 except Exception:
     HERMES_VERSION = "0.0.0"
 
@@ -172,7 +172,7 @@ class HermesACPAgent(acp.Agent):
         provider = getattr(state.agent, "provider", None) or detect_provider() or "openrouter"
 
         try:
-            from hermes_cli.models import curated_models_for_provider, normalize_provider, provider_label
+            from hermes_agent.cli.models.models import curated_models_for_provider, normalize_provider, provider_label
 
             normalized_provider = normalize_provider(provider)
             provider_name = provider_label(normalized_provider)
@@ -235,7 +235,7 @@ class HermesACPAgent(acp.Agent):
         new_model = raw_model.strip()
 
         try:
-            from hermes_cli.models import detect_provider_for_model, parse_model_input
+            from hermes_agent.cli.models.models import detect_provider_for_model, parse_model_input
 
             target_provider, new_model = parse_model_input(new_model, current_provider)
             if target_provider == current_provider:
@@ -257,7 +257,7 @@ class HermesACPAgent(acp.Agent):
             return
 
         try:
-            from tools.mcp_tool import register_mcp_servers
+            from hermes_agent.tools.mcp.tool import register_mcp_servers
 
             config_map: dict[str, dict] = {}
             for server in mcp_servers:
@@ -285,7 +285,7 @@ class HermesACPAgent(acp.Agent):
             return
 
         try:
-            from model_tools import get_tool_definitions
+            from hermes_agent.tools.dispatch import get_tool_definitions
 
             enabled_toolsets = getattr(state.agent, "enabled_toolsets", None) or ["hermes-acp"]
             disabled_toolsets = getattr(state.agent, "disabled_toolsets", None)
@@ -572,7 +572,7 @@ class HermesACPAgent(acp.Agent):
             nonlocal previous_approval_cb, previous_interactive
             if approval_cb:
                 try:
-                    from tools import terminal_tool as _terminal_tool
+                    from hermes_agent.tools import terminal as _terminal_tool
                     previous_approval_cb = _terminal_tool._get_approval_callback()
                     _terminal_tool.set_approval_callback(approval_cb)
                 except Exception:
@@ -599,7 +599,7 @@ class HermesACPAgent(acp.Agent):
                     os.environ["HERMES_INTERACTIVE"] = previous_interactive
                 if approval_cb:
                     try:
-                        from tools import terminal_tool as _terminal_tool
+                        from hermes_agent.tools import terminal as _terminal_tool
                         _terminal_tool.set_approval_callback(previous_approval_cb)
                     except Exception:
                         logger.debug("Could not restore approval callback", exc_info=True)
@@ -618,7 +618,7 @@ class HermesACPAgent(acp.Agent):
         final_response = result.get("final_response", "")
         if final_response:
             try:
-                from agent.title_generator import maybe_auto_title
+                from hermes_agent.agent.title_generator import maybe_auto_title
 
                 maybe_auto_title(
                     self.session_manager._get_db(),
@@ -753,7 +753,7 @@ class HermesACPAgent(acp.Agent):
 
     def _cmd_tools(self, args: str, state: SessionState) -> str:
         try:
-            from model_tools import get_tool_definitions
+            from hermes_agent.tools.dispatch import get_tool_definitions
             toolsets = getattr(state.agent, "enabled_toolsets", None) or ["hermes-acp"]
             tools = get_tool_definitions(enabled_toolsets=toolsets, quiet_mode=True)
             if not tools:
@@ -804,7 +804,7 @@ class HermesACPAgent(acp.Agent):
             if not hasattr(agent, "_compress_context"):
                 return "Context compression not available for this agent."
 
-            from agent.model_metadata import estimate_messages_tokens_rough
+            from hermes_agent.providers.metadata import estimate_messages_tokens_rough
 
             original_count = len(state.history)
             approx_tokens = estimate_messages_tokens_rough(state.history)

hermes_agent/acp/session.py

@@ -8,7 +8,7 @@ history.
 """
 from __future__ import annotations
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 import copy
 import json
@@ -100,7 +100,7 @@ def _register_task_cwd(task_id: str, cwd: str) -> None:
     if not task_id:
         return
     try:
-        from tools.terminal_tool import register_task_env_overrides
+        from hermes_agent.tools.terminal import register_task_env_overrides
         register_task_env_overrides(task_id, {"cwd": cwd})
     except Exception:
         logger.debug("Failed to register ACP task cwd override", exc_info=True)
@@ -111,7 +111,7 @@ def _clear_task_cwd(task_id: str) -> None:
     if not task_id:
         return
     try:
-        from tools.terminal_tool import clear_task_env_overrides
+        from hermes_agent.tools.terminal import clear_task_env_overrides
         clear_task_env_overrides(task_id)
     except Exception:
         logger.debug("Failed to clear ACP task cwd override", exc_info=True)
@@ -355,7 +355,7 @@ class SessionManager:
         if self._db_instance is not None:
             return self._db_instance
         try:
-            from hermes_state import SessionDB
+            from hermes_agent.state import SessionDB
             hermes_home = get_hermes_home()
             self._db_instance = SessionDB(db_path=hermes_home / "state.db")
             return self._db_instance
@@ -523,9 +523,9 @@ class SessionManager:
         if self._agent_factory is not None:
             return self._agent_factory()
 
-        from run_agent import AIAgent
-        from hermes_cli.config import load_config
-        from hermes_cli.runtime_provider import resolve_runtime_provider
+        from hermes_agent.agent.loop import AIAgent
+        from hermes_agent.cli.config import load_config
+        from hermes_agent.cli.runtime_provider import resolve_runtime_provider
 
         config = load_config()
         model_cfg = config.get("model")

hermes_agent/acp/tools.py

@@ -103,7 +103,7 @@ def _build_patch_mode_content(patch_text: str) -> List[Any]:
         return [acp.tool_content(acp.text_block(""))]
 
     try:
-        from tools.patch_parser import OperationType, parse_v4a_patch
+        from hermes_agent.tools.patch_parser import OperationType, parse_v4a_patch
 
         operations, error = parse_v4a_patch(patch_text)
         if error or not operations:
@@ -243,7 +243,7 @@ def _build_tool_complete_content(
 
     if tool_name in {"write_file", "patch", "skill_manage"}:
         try:
-            from agent.display import extract_edit_diff
+            from hermes_agent.agent.display import extract_edit_diff
 
             diff_text = extract_edit_diff(
                 tool_name,

hermes_agent/agent/context/compressor.py

@@ -24,14 +24,14 @@ import re
 import time
 from typing import Any, Dict, List, Optional
 
-from agent.auxiliary_client import call_llm
-from agent.context_engine import ContextEngine
-from agent.model_metadata import (
+from hermes_agent.providers.auxiliary import call_llm
+from hermes_agent.agent.context.engine import ContextEngine
+from hermes_agent.providers.metadata import (
     MINIMUM_CONTEXT_LENGTH,
     get_model_context_length,
     estimate_messages_tokens_rough,
 )
-from agent.redact import redact_sensitive_text
+from hermes_agent.agent.redact import redact_sensitive_text
 
 logger = logging.getLogger(__name__)
 

hermes_agent/agent/context/references.py

@@ -11,7 +11,7 @@ from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Awaitable, Callable
 
-from agent.model_metadata import estimate_tokens_rough
+from hermes_agent.providers.metadata import estimate_tokens_rough
 
 _QUOTED_REFERENCE_VALUE = r'(?:`[^`\n]+`|"[^"\n]+"|\'[^\'\n]+\')'
 REFERENCE_PATTERN = re.compile(
@@ -315,7 +315,7 @@ async def _fetch_url_content(
 
 
 async def _default_url_fetcher(url: str) -> str:
-    from tools.web_tools import web_extract_tool
+    from hermes_agent.tools.web import web_extract_tool
 
     raw = await web_extract_tool([url], format="markdown", use_llm_processing=True)
     payload = json.loads(raw)
@@ -340,7 +340,7 @@ def _resolve_path(cwd: Path, target: str, *, allowed_root: Path | None = None) -
 
 
 def _ensure_reference_path_allowed(path: Path) -> None:
-    from hermes_constants import get_hermes_home
+    from hermes_agent.constants import get_hermes_home
     home = Path(os.path.expanduser("~")).resolve()
     hermes_home = get_hermes_home().resolve()
 

hermes_agent/agent/copilot_acp_client.py

@@ -21,8 +21,8 @@ from pathlib import Path
 from types import SimpleNamespace
 from typing import Any
 
-from agent.file_safety import get_read_block_error, is_write_denied
-from agent.redact import redact_sensitive_text
+from hermes_agent.agent.file_safety import get_read_block_error, is_write_denied
+from hermes_agent.agent.redact import redact_sensitive_text
 
 ACP_MARKER_BASE_URL = "acp://copilot"
 _DEFAULT_TIMEOUT_SECONDS = 900.0

hermes_agent/agent/display.py

@@ -13,7 +13,7 @@ from dataclasses import dataclass, field
 from difflib import unified_diff
 from pathlib import Path
 
-from utils import safe_json_loads
+from hermes_agent.utils import safe_json_loads
 
 # ANSI escape codes for coloring tool failure indicators
 _RED = "\033[31m"
@@ -43,7 +43,7 @@ def _diff_ansi() -> dict[str, str]:
     plus = "\033[38;2;255;255;255;48;2;20;90;20m"
 
     try:
-        from hermes_cli.skin_engine import get_active_skin
+        from hermes_agent.cli.ui.skin_engine import get_active_skin
         skin = get_active_skin()
 
         def _hex_fg(key: str, fallback_rgb: tuple[int, int, int]) -> str:
@@ -118,7 +118,7 @@ def get_tool_preview_max_len() -> int:
 def _get_skin():
     """Get the active skin config, or None if not available."""
     try:
-        from hermes_cli.skin_engine import get_active_skin
+        from hermes_agent.cli.ui.skin_engine import get_active_skin
         return get_active_skin()
     except Exception:
         return None
@@ -148,7 +148,7 @@ def get_tool_emoji(tool_name: str, default: str = "⚡") -> str:
             return override
     # 2. Registry default
     try:
-        from tools.registry import registry
+        from hermes_agent.tools.registry import registry
         emoji = registry.get_emoji(tool_name, default="")
         if emoji:
             return emoji
@@ -311,7 +311,7 @@ def _resolve_skill_manage_paths(args: dict) -> list[Path]:
     if not action or not name:
         return []
 
-    from tools.skill_manager_tool import _find_skill, _resolve_skill_dir
+    from hermes_agent.tools.skills.manager import _find_skill, _resolve_skill_dir
 
     if action == "create":
         skill_dir = _resolve_skill_dir(name, args.get("category"))
@@ -729,6 +729,7 @@ class KawaiiSpinner:
                 time.sleep(0.1)
                 continue
             frame = self.spinner_frames[self.frame_idx % len(self.spinner_frames)]
+            assert self.start_time is not None  # start() sets it before thread starts
             elapsed = time.time() - self.start_time
             if wings:
                 left, right = wings[self.frame_idx % len(wings)]

hermes_agent/agent/file_safety.py

@@ -10,7 +10,7 @@ from typing import Optional
 def _hermes_home_path() -> Path:
     """Resolve the active HERMES_HOME (profile-aware) without circular imports."""
     try:
-        from hermes_constants import get_hermes_home  # local import to avoid cycles
+        from hermes_agent.constants import get_hermes_home  # local import to avoid cycles
         return get_hermes_home()
     except Exception:
         return Path(os.path.expanduser("~/.hermes"))

hermes_agent/agent/image_gen/provider.py

@@ -164,7 +164,7 @@ def resolve_aspect_ratio(value: Optional[str]) -> str:
 
 def _images_cache_dir() -> Path:
     """Return ``$HERMES_HOME/cache/images/``, creating parents as needed."""
-    from hermes_constants import get_hermes_home
+    from hermes_agent.constants import get_hermes_home
 
     path = get_hermes_home() / "cache" / "images"
     path.mkdir(parents=True, exist_ok=True)

hermes_agent/agent/image_gen/registry.py

@@ -24,7 +24,7 @@ import logging
 import threading
 from typing import Dict, List, Optional
 
-from agent.image_gen_provider import ImageGenProvider
+from hermes_agent.agent.image_gen.provider import ImageGenProvider
 
 logger = logging.getLogger(__name__)
 
@@ -80,7 +80,7 @@ def get_active_provider() -> Optional[ImageGenProvider]:
     """
     configured: Optional[str] = None
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
 
         cfg = load_config()
         section = cfg.get("image_gen") if isinstance(cfg, dict) else None

hermes_agent/agent/insights.py

@@ -10,7 +10,7 @@ multi-platform architecture with additional cost estimation and platform
 breakdown capabilities.
 
 Usage:
-    from agent.insights import InsightsEngine
+    from hermes_agent.agent.insights import InsightsEngine
     engine = InsightsEngine(db)
     report = engine.generate(days=30)
     print(engine.format_terminal(report))
@@ -22,7 +22,7 @@ from collections import Counter, defaultdict
 from datetime import datetime
 from typing import Any, Dict, List
 
-from agent.usage_pricing import (
+from hermes_agent.providers.pricing import (
     CanonicalUsage,
     DEFAULT_PRICING,
     estimate_usage_cost,

hermes_agent/agent/loop.py

@@ -14,7 +14,7 @@ Features:
 - Support for multiple model providers
 
 Usage:
-    from run_agent import AIAgent
+    from hermes_agent.agent.loop import AIAgent
     
     agent = AIAgent(base_url="http://localhost:30000/v1", model="claude-opus-4-20250514")
     response = agent.run_conversation("Tell me about the latest Python updates")
@@ -37,18 +37,21 @@ import time
 import threading
 from types import SimpleNamespace
 import uuid
-from typing import List, Dict, Any, Optional
+from typing import Callable, List, Dict, Any, Optional, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from hermes_agent.providers.rate_limiting import RateLimitState
 from openai import OpenAI
 import fire
 from datetime import datetime
 from pathlib import Path
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 # Load .env from ~/.hermes/.env first, then project root as dev fallback.
 # User-managed env files should override stale shell exports on restart.
-from hermes_cli.env_loader import load_hermes_dotenv
-from hermes_cli.timeouts import (
+from hermes_agent.cli.env_loader import load_hermes_dotenv
+from hermes_agent.cli.timeouts import (
     get_provider_request_timeout,
     get_provider_stale_timeout,
 )
@@ -64,30 +67,30 @@ else:
 
 
 # Import our tool system
-from model_tools import (
+from hermes_agent.tools.dispatch import (
     get_tool_definitions,
     get_toolset_for_tool,
     handle_function_call,
     check_toolset_requirements,
 )
-from tools.terminal_tool import cleanup_vm, get_active_env, is_persistent_env
-from tools.tool_result_storage import maybe_persist_tool_result, enforce_turn_budget
-from tools.interrupt import set_interrupt as _set_interrupt
-from tools.browser_tool import cleanup_browser
+from hermes_agent.tools.terminal import cleanup_vm, get_active_env, is_persistent_env
+from hermes_agent.tools.result_storage import maybe_persist_tool_result, enforce_turn_budget
+from hermes_agent.tools.interrupt import set_interrupt as _set_interrupt
+from hermes_agent.tools.browser.tool import cleanup_browser
 
 
-from hermes_constants import OPENROUTER_BASE_URL
+from hermes_agent.constants import OPENROUTER_BASE_URL
 
 # Agent internals extracted to agent/ package for modularity
-from agent.memory_manager import build_memory_context_block, sanitize_context
-from agent.retry_utils import jittered_backoff
-from agent.error_classifier import classify_api_error, FailoverReason
-from agent.prompt_builder import (
+from hermes_agent.agent.memory.manager import build_memory_context_block, sanitize_context
+from hermes_agent.providers.retry import jittered_backoff
+from hermes_agent.providers.errors import classify_api_error, FailoverReason
+from hermes_agent.agent.prompt_builder import (
     DEFAULT_AGENT_IDENTITY, PLATFORM_HINTS,
     MEMORY_GUIDANCE, SESSION_SEARCH_GUIDANCE, SKILLS_GUIDANCE,
     build_nous_subscription_prompt,
 )
-from agent.model_metadata import (
+from hermes_agent.providers.metadata import (
     fetch_model_metadata,
     estimate_tokens_rough, estimate_messages_tokens_rough, estimate_request_tokens_rough,
     get_next_probe_tier, parse_context_limit_from_error,
@@ -95,12 +98,12 @@ from agent.model_metadata import (
     save_context_length, is_local_endpoint,
     query_ollama_num_ctx,
 )
-from agent.context_compressor import ContextCompressor
-from agent.subdirectory_hints import SubdirectoryHintTracker
-from agent.prompt_caching import apply_anthropic_cache_control
-from agent.prompt_builder import build_skills_system_prompt, build_context_files_prompt, build_environment_hints, load_soul_md, TOOL_USE_ENFORCEMENT_GUIDANCE, TOOL_USE_ENFORCEMENT_MODELS, DEVELOPER_ROLE_MODELS, GOOGLE_MODEL_OPERATIONAL_GUIDANCE, OPENAI_MODEL_EXECUTION_GUIDANCE
-from agent.usage_pricing import estimate_usage_cost, normalize_usage
-from agent.codex_responses_adapter import (
+from hermes_agent.agent.context.compressor import ContextCompressor
+from hermes_agent.agent.subdirectory_hints import SubdirectoryHintTracker
+from hermes_agent.providers.caching import apply_anthropic_cache_control
+from hermes_agent.agent.prompt_builder import build_skills_system_prompt, build_context_files_prompt, build_environment_hints, load_soul_md, TOOL_USE_ENFORCEMENT_GUIDANCE, TOOL_USE_ENFORCEMENT_MODELS, DEVELOPER_ROLE_MODELS, GOOGLE_MODEL_OPERATIONAL_GUIDANCE, OPENAI_MODEL_EXECUTION_GUIDANCE
+from hermes_agent.providers.pricing import estimate_usage_cost, normalize_usage
+from hermes_agent.providers.codex_adapter import (
     _chat_content_to_responses_parts,
     _chat_messages_to_responses_input as _codex_chat_messages_to_responses_input,
     _derive_responses_function_call_id as _codex_derive_responses_function_call_id,
@@ -114,17 +117,17 @@ from agent.codex_responses_adapter import (
     _split_responses_tool_id as _codex_split_responses_tool_id,
     _summarize_user_message_for_log,
 )
-from agent.display import (
+from hermes_agent.agent.display import (
     KawaiiSpinner, build_tool_preview as _build_tool_preview,
     get_cute_tool_message as _get_cute_tool_message_impl,
     _detect_tool_failure,
     get_tool_emoji as _get_tool_emoji,
 )
-from agent.trajectory import (
+from hermes_agent.agent.trajectory import (
     convert_scratchpad_to_think, has_incomplete_scratchpad,
     save_trajectory as _save_trajectory_to_file,
 )
-from utils import atomic_json_write, base_url_host_matches, base_url_hostname, env_var_enabled, normalize_proxy_url
+from hermes_agent.utils import atomic_json_write, base_url_host_matches, base_url_hostname, env_var_enabled, normalize_proxy_url
 
 
 
@@ -733,17 +736,17 @@ class AIAgent:
         provider_require_parameters: bool = False,
         provider_data_collection: str = None,
         session_id: str = None,
-        tool_progress_callback: callable = None,
-        tool_start_callback: callable = None,
-        tool_complete_callback: callable = None,
-        thinking_callback: callable = None,
-        reasoning_callback: callable = None,
-        clarify_callback: callable = None,
-        step_callback: callable = None,
-        stream_delta_callback: callable = None,
-        interim_assistant_callback: callable = None,
-        tool_gen_callback: callable = None,
-        status_callback: callable = None,
+        tool_progress_callback: Callable[..., Any] = None,
+        tool_start_callback: Callable[..., Any] = None,
+        tool_complete_callback: Callable[..., Any] = None,
+        thinking_callback: Callable[..., Any] = None,
+        reasoning_callback: Callable[..., Any] = None,
+        clarify_callback: Callable[..., Any] = None,
+        step_callback: Callable[..., Any] = None,
+        stream_delta_callback: Callable[..., Any] = None,
+        interim_assistant_callback: Callable[..., Any] = None,
+        tool_gen_callback: Callable[..., Any] = None,
+        status_callback: Callable[..., Any] = None,
         max_tokens: int = None,
         reasoning_config: Dict[str, Any] = None,
         service_tier: str = None,
@@ -873,7 +876,7 @@ class AIAgent:
             self.api_mode = "chat_completions"
 
         try:
-            from hermes_cli.model_normalize import (
+            from hermes_agent.cli.models.normalize import (
                 _AGGREGATOR_PROVIDERS,
                 normalize_model_for_provider,
             )
@@ -1023,7 +1026,7 @@ class AIAgent:
         # Centralized logging — agent.log (INFO+) and errors.log (WARNING+)
         # both live under ~/.hermes/logs/.  Idempotent, so gateway mode
         # (which creates a new AIAgent per message) won't duplicate handlers.
-        from hermes_logging import setup_logging, setup_verbose_logging
+        from hermes_agent.logging import setup_logging, setup_verbose_logging
         setup_logging(hermes_home=_hermes_home)
 
         if self.verbose_logging:
@@ -1037,10 +1040,10 @@ class AIAgent:
                 # File handlers (agent.log, errors.log) still capture everything.
                 for quiet_logger in [
                     'tools',               # all tools.* (terminal, browser, web, file, etc.)
-                    'run_agent',            # agent runner internals
-                    'trajectory_compressor',
+                    'hermes_agent.agent.loop',            # agent runner internals
+                    'scripts.trajectory_compressor',
                     'cron',                 # scheduler (only relevant in daemon mode)
-                    'hermes_cli',           # CLI helpers
+                    'hermes_agent.cli',           # CLI helpers
                 ]:
                     logging.getLogger(quiet_logger).setLevel(logging.ERROR)
         
@@ -1082,12 +1085,12 @@ class AIAgent:
         _provider_timeout = get_provider_request_timeout(self.provider, self.model)
 
         if self.api_mode == "anthropic_messages":
-            from agent.anthropic_adapter import build_anthropic_client, resolve_anthropic_token
+            from hermes_agent.providers.anthropic_adapter import build_anthropic_client, resolve_anthropic_token
             # Bedrock + Claude → use AnthropicBedrock SDK for full feature parity
             # (prompt caching, thinking budgets, adaptive thinking).
             _is_bedrock_anthropic = self.provider == "bedrock"
             if _is_bedrock_anthropic:
-                from agent.anthropic_adapter import build_anthropic_bedrock_client
+                from hermes_agent.providers.anthropic_adapter import build_anthropic_bedrock_client
                 _region_match = re.search(r"bedrock-runtime\.([a-z0-9-]+)\.", base_url or "")
                 _br_region = _region_match.group(1) if _region_match else "us-east-1"
                 self._bedrock_region = _br_region
@@ -1116,7 +1119,7 @@ class AIAgent:
                 # so injects Claude-Code identity headers and system prompts
                 # that cause 401/403 on their endpoints.  Guards #1739 and
                 # the third-party identity-injection bug.
-                from agent.anthropic_adapter import _is_oauth_token as _is_oat
+                from hermes_agent.providers.anthropic_adapter import _is_oauth_token as _is_oat
                 self._is_anthropic_oauth = _is_oat(effective_key) if _is_native_anthropic else False
                 self._anthropic_client = build_anthropic_client(effective_key, base_url, timeout=_provider_timeout)
                 # No OpenAI client needed for Anthropic mode
@@ -1134,7 +1137,7 @@ class AIAgent:
             # Guardrail config — read from config.yaml at init time.
             self._bedrock_guardrail_config = None
             try:
-                from hermes_cli.config import load_config as _load_br_cfg
+                from hermes_agent.cli.config import load_config as _load_br_cfg
                 _gr = _load_br_cfg().get("bedrock", {}).get("guardrail", {})
                 if _gr.get("guardrail_identifier") and _gr.get("guardrail_version"):
                     self._bedrock_guardrail_config = {
@@ -1170,7 +1173,7 @@ class AIAgent:
                         "X-OpenRouter-Categories": "productivity,cli-agent",
                     }
                 elif base_url_host_matches(effective_base, "api.githubcopilot.com"):
-                    from hermes_cli.models import copilot_default_headers
+                    from hermes_agent.cli.models.models import copilot_default_headers
 
                     client_kwargs["default_headers"] = copilot_default_headers()
                 elif base_url_host_matches(effective_base, "api.kimi.com"):
@@ -1180,11 +1183,11 @@ class AIAgent:
                 elif base_url_host_matches(effective_base, "portal.qwen.ai"):
                     client_kwargs["default_headers"] = _qwen_portal_headers()
                 elif base_url_host_matches(effective_base, "chatgpt.com"):
-                    from agent.auxiliary_client import _codex_cloudflare_headers
+                    from hermes_agent.providers.auxiliary import _codex_cloudflare_headers
                     client_kwargs["default_headers"] = _codex_cloudflare_headers(api_key)
             else:
                 # No explicit creds — use the centralized provider router
-                from agent.auxiliary_client import resolve_provider_client
+                from hermes_agent.providers.auxiliary import resolve_provider_client
                 _routed_client, _ = resolve_provider_client(
                     self.provider or "auto", model=self.model, raw_codex=True)
                 if _routed_client is not None:
@@ -1208,7 +1211,7 @@ class AIAgent:
                         # (e.g. alibaba → DASHSCOPE_API_KEY, not ALIBABA_API_KEY).
                         _env_hint = f"{_explicit.upper()}_API_KEY"
                         try:
-                            from hermes_cli.auth import PROVIDER_REGISTRY
+                            from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
                             _pcfg = PROVIDER_REGISTRY.get(_explicit)
                             if _pcfg and _pcfg.api_key_env_vars:
                                 _env_hint = _pcfg.api_key_env_vars[0]
@@ -1361,7 +1364,7 @@ class AIAgent:
         self._cached_system_prompt: Optional[str] = None
         
         # Filesystem checkpoint manager (transparent — not a tool)
-        from tools.checkpoint_manager import CheckpointManager
+        from hermes_agent.tools.checkpoint import CheckpointManager
         self._checkpoint_mgr = CheckpointManager(
             enabled=checkpoints_enabled,
             max_snapshots=checkpoint_max_snapshots,
@@ -1397,12 +1400,12 @@ class AIAgent:
                 )
         
         # In-memory todo list for task planning (one per agent/session)
-        from tools.todo_tool import TodoStore
+        from hermes_agent.tools.todo import TodoStore
         self._todo_store = TodoStore()
         
         # Load config once for memory, skills, and compression sections
         try:
-            from hermes_cli.config import load_config as _load_agent_config
+            from hermes_agent.cli.config import load_config as _load_agent_config
             _agent_cfg = _load_agent_config()
         except Exception:
             _agent_cfg = {}
@@ -1427,7 +1430,7 @@ class AIAgent:
                 self._memory_nudge_interval = int(mem_config.get("nudge_interval", 10))
                 self._memory_flush_min_turns = int(mem_config.get("flush_min_turns", 6))
                 if self._memory_enabled or self._user_profile_enabled:
-                    from tools.memory_tool import MemoryStore
+                    from hermes_agent.tools.memory import MemoryStore
                     self._memory_store = MemoryStore(
                         memory_char_limit=mem_config.get("memory_char_limit", 2200),
                         user_char_limit=mem_config.get("user_char_limit", 1375),
@@ -1446,8 +1449,8 @@ class AIAgent:
                 _mem_provider_name = mem_config.get("provider", "") if mem_config else ""
 
                 if _mem_provider_name:
-                    from agent.memory_manager import MemoryManager as _MemoryManager
-                    from plugins.memory import load_memory_provider as _load_mem
+                    from hermes_agent.agent.memory.manager import MemoryManager as _MemoryManager
+                    from hermes_agent.plugins.memory import load_memory_provider as _load_mem
                     self._memory_manager = _MemoryManager()
                     _mp = _load_mem(_mem_provider_name)
                     if _mp and _mp.is_available():
@@ -1476,7 +1479,7 @@ class AIAgent:
                             _init_kwargs["gateway_session_key"] = self._gateway_session_key
                         # Profile identity for per-profile provider scoping
                         try:
-                            from hermes_cli.profiles import get_active_profile_name
+                            from hermes_agent.cli.profiles import get_active_profile_name
                             _profile = get_active_profile_name()
                             _init_kwargs["agent_identity"] = _profile
                             _init_kwargs["agent_workspace"] = "hermes"
@@ -1587,7 +1590,7 @@ class AIAgent:
         # Check custom_providers per-model context_length
         if _config_context_length is None:
             try:
-                from hermes_cli.config import get_compatible_custom_providers
+                from hermes_agent.cli.config import get_compatible_custom_providers
                 _custom_providers = get_compatible_custom_providers(_agent_cfg)
             except Exception:
                 _custom_providers = _agent_cfg.get("custom_providers")
@@ -1638,7 +1641,7 @@ class AIAgent:
         if _engine_name != "compressor":
             # Try loading from plugins/context_engine/<name>/
             try:
-                from plugins.context_engine import load_context_engine
+                from hermes_agent.plugins.context_engine import load_context_engine
                 _selected_engine = load_context_engine(_engine_name)
             except Exception as _ce_load_err:
                 logger.debug("Context engine load from plugins/context_engine/: %s", _ce_load_err)
@@ -1646,7 +1649,7 @@ class AIAgent:
             # Try general plugin system as fallback
             if _selected_engine is None:
                 try:
-                    from hermes_cli.plugins import get_plugin_context_engine
+                    from hermes_agent.cli.plugins import get_plugin_context_engine
                     _candidate = get_plugin_context_engine()
                     if _candidate and _candidate.name == _engine_name:
                         _selected_engine = _candidate
@@ -1663,7 +1666,7 @@ class AIAgent:
         if _selected_engine is not None:
             self.context_compressor = _selected_engine
             # Resolve context_length for plugin engines — mirrors switch_model() path
-            from agent.model_metadata import get_model_context_length
+            from hermes_agent.providers.metadata import get_model_context_length
             _plugin_ctx_len = get_model_context_length(
                 self.model,
                 base_url=self.base_url,
@@ -1699,7 +1702,7 @@ class AIAgent:
 
         # Reject models whose context window is below the minimum required
         # for reliable tool-calling workflows (64K tokens).
-        from agent.model_metadata import MINIMUM_CONTEXT_LENGTH
+        from hermes_agent.providers.metadata import MINIMUM_CONTEXT_LENGTH
         _ctx = getattr(self.context_compressor, "context_length", 0)
         if _ctx and _ctx < MINIMUM_CONTEXT_LENGTH:
             raise ValueError(
@@ -1876,7 +1879,7 @@ class AIAgent:
         change persists across turns (unlike fallback which is
         turn-scoped).
         """
-        from hermes_cli.providers import determine_api_mode
+        from hermes_agent.cli.providers import determine_api_mode
 
         # ── Determine api_mode if not provided ──
         if not api_mode:
@@ -1908,7 +1911,7 @@ class AIAgent:
 
         # ── Build new client ──
         if api_mode == "anthropic_messages":
-            from agent.anthropic_adapter import (
+            from hermes_agent.providers.anthropic_adapter import (
                 build_anthropic_client,
                 resolve_anthropic_token,
                 _is_oauth_token,
@@ -1956,7 +1959,7 @@ class AIAgent:
 
         # ── Update context compressor ──
         if hasattr(self, "context_compressor") and self.context_compressor:
-            from agent.model_metadata import get_model_context_length
+            from hermes_agent.providers.metadata import get_model_context_length
             new_context_length = get_model_context_length(
                 self.model,
                 base_url=self.base_url,
@@ -2151,8 +2154,8 @@ class AIAgent:
         if not self.compression_enabled:
             return
         try:
-            from agent.auxiliary_client import get_text_auxiliary_client
-            from agent.model_metadata import (
+            from hermes_agent.providers.auxiliary import get_text_auxiliary_client
+            from hermes_agent.providers.metadata import (
                 MINIMUM_CONTEXT_LENGTH,
                 get_model_context_length,
             )
@@ -2445,7 +2448,7 @@ class AIAgent:
         normalized_provider = (provider or "").strip().lower()
         if normalized_provider == "copilot":
             try:
-                from hermes_cli.models import _should_use_copilot_responses_api
+                from hermes_agent.cli.models.models import _should_use_copilot_responses_api
                 return _should_use_copilot_responses_api(model)
             except Exception:
                 # Fall back to the generic GPT-5 rule if Copilot-specific
@@ -3753,7 +3756,7 @@ class AIAgent:
         if not headers:
             return
         try:
-            from agent.rate_limit_tracker import parse_rate_limit_headers
+            from hermes_agent.providers.rate_limiting import parse_rate_limit_headers
             state = parse_rate_limit_headers(headers, provider=self.provider)
             if state is not None:
                 self._rate_limit_state = state
@@ -3885,7 +3888,7 @@ class AIAgent:
 
         # 1. Kill background processes for this task
         try:
-            from tools.process_registry import process_registry
+            from hermes_agent.tools.process_registry import process_registry
             process_registry.kill_all(task_id=task_id)
         except Exception:
             pass
@@ -4102,7 +4105,7 @@ class AIAgent:
             if context_files_prompt:
                 prompt_parts.append(context_files_prompt)
 
-        from hermes_time import now as _hermes_now
+        from hermes_agent.time import now as _hermes_now
         now = _hermes_now()
         timestamp_line = f"Conversation started: {now.strftime('%A, %B %d, %Y %I:%M %p')}"
         if self.pass_session_id and self.session_id:
@@ -4230,7 +4233,7 @@ class AIAgent:
 
         Returns the original list if no truncation was needed.
         """
-        from tools.delegate_tool import _get_max_concurrent_children
+        from hermes_agent.tools.delegate import _get_max_concurrent_children
         max_children = _get_max_concurrent_children()
         delegate_count = sum(1 for tc in tool_calls if tc.function.name == "delegate_task")
         if delegate_count <= max_children:
@@ -4406,7 +4409,7 @@ class AIAgent:
             return None
 
     def _create_openai_client(self, client_kwargs: dict, *, reason: str, shared: bool) -> Any:
-        from agent.auxiliary_client import _validate_base_url, _validate_proxy_env_urls
+        from hermes_agent.providers.auxiliary import _validate_base_url, _validate_proxy_env_urls
         # Treat client_kwargs as read-only. Callers pass self._client_kwargs (or shallow
         # copies of it) in; any in-place mutation leaks back into the stored dict and is
         # reused on subsequent requests. #10933 hit this by injecting an httpx.Client
@@ -4419,7 +4422,7 @@ class AIAgent:
         _validate_proxy_env_urls()
         _validate_base_url(client_kwargs.get("base_url"))
         if self.provider == "copilot-acp" or str(client_kwargs.get("base_url", "")).startswith("acp://copilot"):
-            from agent.copilot_acp_client import CopilotACPClient
+            from hermes_agent.agent.copilot_acp_client import CopilotACPClient
 
             client = CopilotACPClient(**client_kwargs)
             logger.info(
@@ -4430,7 +4433,7 @@ class AIAgent:
             )
             return client
         if self.provider == "google-gemini-cli" or str(client_kwargs.get("base_url", "")).startswith("cloudcode-pa://"):
-            from agent.gemini_cloudcode_adapter import GeminiCloudCodeClient
+            from hermes_agent.providers.gemini_cloudcode_adapter import GeminiCloudCodeClient
 
             # Strip OpenAI-specific kwargs the Gemini client doesn't accept
             safe_kwargs = {
@@ -4446,7 +4449,7 @@ class AIAgent:
             )
             return client
         if self.provider == "gemini":
-            from agent.gemini_native_adapter import GeminiNativeClient, is_native_gemini_base_url
+            from hermes_agent.providers.gemini_adapter import GeminiNativeClient, is_native_gemini_base_url
 
             base_url = str(client_kwargs.get("base_url", "") or "")
             if is_native_gemini_base_url(base_url):
@@ -4695,7 +4698,7 @@ class AIAgent:
     def _close_request_openai_client(self, client: Any, *, reason: str) -> None:
         self._close_openai_client(client, reason=reason, shared=False)
 
-    def _run_codex_stream(self, api_kwargs: dict, client: Any = None, on_first_delta: callable = None):
+    def _run_codex_stream(self, api_kwargs: dict, client: Any = None, on_first_delta: Callable[..., Any] = None):
         """Execute one streaming Responses API request and return the final response."""
         import httpx as _httpx
 
@@ -4901,7 +4904,7 @@ class AIAgent:
             return False
 
         try:
-            from hermes_cli.auth import resolve_codex_runtime_credentials
+            from hermes_agent.cli.auth.auth import resolve_codex_runtime_credentials
 
             creds = resolve_codex_runtime_credentials(force_refresh=force)
         except Exception as exc:
@@ -4930,7 +4933,7 @@ class AIAgent:
             return False
 
         try:
-            from hermes_cli.auth import resolve_nous_runtime_credentials
+            from hermes_agent.cli.auth.auth import resolve_nous_runtime_credentials
 
             creds = resolve_nous_runtime_credentials(
                 min_key_ttl_seconds=max(60, int(os.getenv("HERMES_NOUS_MIN_KEY_TTL_SECONDS", "1800"))),
@@ -4969,7 +4972,7 @@ class AIAgent:
             return False
 
         try:
-            from agent.anthropic_adapter import resolve_anthropic_token, build_anthropic_client
+            from hermes_agent.providers.anthropic_adapter import resolve_anthropic_token, build_anthropic_client
 
             new_token = resolve_anthropic_token()
         except Exception as exc:
@@ -5002,19 +5005,19 @@ class AIAgent:
         # Only treat as OAuth on native Anthropic; third-party endpoints using
         # the Anthropic protocol must not trip OAuth paths (#1739 & third-party
         # identity-injection guard).
-        from agent.anthropic_adapter import _is_oauth_token
+        from hermes_agent.providers.anthropic_adapter import _is_oauth_token
         self._is_anthropic_oauth = _is_oauth_token(new_token) if self.provider == "anthropic" else False
         return True
 
     def _apply_client_headers_for_base_url(self, base_url: str) -> None:
-        from agent.auxiliary_client import _AI_GATEWAY_HEADERS, _OR_HEADERS
+        from hermes_agent.providers.auxiliary import _AI_GATEWAY_HEADERS, _OR_HEADERS
 
         if base_url_host_matches(base_url, "openrouter.ai"):
             self._client_kwargs["default_headers"] = dict(_OR_HEADERS)
         elif base_url_host_matches(base_url, "ai-gateway.vercel.sh"):
             self._client_kwargs["default_headers"] = dict(_AI_GATEWAY_HEADERS)
         elif base_url_host_matches(base_url, "api.githubcopilot.com"):
-            from hermes_cli.models import copilot_default_headers
+            from hermes_agent.cli.models.models import copilot_default_headers
 
             self._client_kwargs["default_headers"] = copilot_default_headers()
         elif base_url_host_matches(base_url, "api.kimi.com"):
@@ -5022,7 +5025,7 @@ class AIAgent:
         elif base_url_host_matches(base_url, "portal.qwen.ai"):
             self._client_kwargs["default_headers"] = _qwen_portal_headers()
         elif base_url_host_matches(base_url, "chatgpt.com"):
-            from agent.auxiliary_client import _codex_cloudflare_headers
+            from hermes_agent.providers.auxiliary import _codex_cloudflare_headers
             self._client_kwargs["default_headers"] = _codex_cloudflare_headers(
                 self._client_kwargs.get("api_key", "")
             )
@@ -5034,7 +5037,7 @@ class AIAgent:
         runtime_base = getattr(entry, "runtime_base_url", None) or getattr(entry, "base_url", None) or self.base_url
 
         if self.api_mode == "anthropic_messages":
-            from agent.anthropic_adapter import build_anthropic_client, _is_oauth_token
+            from hermes_agent.providers.anthropic_adapter import build_anthropic_client, _is_oauth_token
 
             try:
                 self._anthropic_client.close()
@@ -5178,7 +5181,7 @@ class AIAgent:
                     result["response"] = self._anthropic_messages_create(api_kwargs)
                 elif self.api_mode == "bedrock_converse":
                     # Bedrock uses boto3 directly — no OpenAI client needed.
-                    from agent.bedrock_adapter import (
+                    from hermes_agent.providers.bedrock_adapter import (
                         _get_bedrock_runtime_client,
                         normalize_converse_response,
                     )
@@ -5243,7 +5246,7 @@ class AIAgent:
                 )
                 try:
                     if self.api_mode == "anthropic_messages":
-                        from agent.anthropic_adapter import build_anthropic_client
+                        from hermes_agent.providers.anthropic_adapter import build_anthropic_client
 
                         self._anthropic_client.close()
                         self._anthropic_client = build_anthropic_client(
@@ -5275,7 +5278,7 @@ class AIAgent:
                 # seed future retries.
                 try:
                     if self.api_mode == "anthropic_messages":
-                        from agent.anthropic_adapter import build_anthropic_client
+                        from hermes_agent.providers.anthropic_adapter import build_anthropic_client
 
                         self._anthropic_client.close()
                         self._anthropic_client = build_anthropic_client(
@@ -5391,7 +5394,7 @@ class AIAgent:
         )
 
     def _interruptible_streaming_api_call(
-        self, api_kwargs: dict, *, on_first_delta: callable = None
+        self, api_kwargs: dict, *, on_first_delta: Callable[..., Any] = None
     ):
         """Streaming variant of _interruptible_api_call for real-time token delivery.
 
@@ -5436,7 +5439,7 @@ class AIAgent:
 
             def _bedrock_call():
                 try:
-                    from agent.bedrock_adapter import (
+                    from hermes_agent.providers.bedrock_adapter import (
                         _get_bedrock_runtime_client,
                         stream_converse_with_callbacks,
                     )
@@ -6016,7 +6019,7 @@ class AIAgent:
             if self._interrupt_requested:
                 try:
                     if self.api_mode == "anthropic_messages":
-                        from agent.anthropic_adapter import build_anthropic_client
+                        from hermes_agent.providers.anthropic_adapter import build_anthropic_client
 
                         self._anthropic_client.close()
                         self._anthropic_client = build_anthropic_client(
@@ -6126,7 +6129,7 @@ class AIAgent:
         # raw_codex=True because the main agent needs direct responses.stream()
         # access for Codex providers.
         try:
-            from agent.auxiliary_client import resolve_provider_client
+            from hermes_agent.providers.auxiliary import resolve_provider_client
             # Pass base_url and api_key from fallback config so custom
             # endpoints (e.g. Ollama Cloud) resolve correctly instead of
             # falling through to OpenRouter defaults.
@@ -6147,7 +6150,7 @@ class AIAgent:
                     fb_provider)
                 return self._try_activate_fallback()  # try next in chain
             try:
-                from hermes_cli.model_normalize import normalize_model_for_provider
+                from hermes_agent.cli.models.normalize import normalize_model_for_provider
 
                 fb_model = normalize_model_for_provider(fb_model, fb_provider)
             except Exception:
@@ -6190,7 +6193,7 @@ class AIAgent:
 
             if fb_api_mode == "anthropic_messages":
                 # Build native Anthropic client instead of using OpenAI client
-                from agent.anthropic_adapter import build_anthropic_client, resolve_anthropic_token, _is_oauth_token
+                from hermes_agent.providers.anthropic_adapter import build_anthropic_client, resolve_anthropic_token, _is_oauth_token
                 effective_key = (fb_client.api_key or resolve_anthropic_token() or "") if fb_provider == "anthropic" else (fb_client.api_key or "")
                 self.api_key = effective_key
                 self._anthropic_api_key = effective_key
@@ -6243,7 +6246,7 @@ class AIAgent:
             # context window (e.g. 200K) instead of the fallback's (e.g. 32K),
             # causing oversized sessions to overflow the fallback.
             if hasattr(self, 'context_compressor') and self.context_compressor:
-                from agent.model_metadata import get_model_context_length
+                from hermes_agent.providers.metadata import get_model_context_length
                 fb_context_length = get_model_context_length(
                     self.model, base_url=self.base_url,
                     api_key=self.api_key, provider=self.provider,
@@ -6304,7 +6307,7 @@ class AIAgent:
 
             # ── Rebuild client for the primary provider ──
             if self.api_mode == "anthropic_messages":
-                from agent.anthropic_adapter import build_anthropic_client
+                from hermes_agent.providers.anthropic_adapter import build_anthropic_client
                 self._anthropic_api_key = rt["anthropic_api_key"]
                 self._anthropic_base_url = rt["anthropic_base_url"]
                 self._anthropic_client = build_anthropic_client(
@@ -6401,7 +6404,7 @@ class AIAgent:
             self.api_key = rt["api_key"]
 
             if self.api_mode == "anthropic_messages":
-                from agent.anthropic_adapter import build_anthropic_client
+                from hermes_agent.providers.anthropic_adapter import build_anthropic_client
                 self._anthropic_api_key = rt["anthropic_api_key"]
                 self._anthropic_base_url = rt["anthropic_base_url"]
                 self._anthropic_client = build_anthropic_client(
@@ -6484,7 +6487,7 @@ class AIAgent:
 
         description = ""
         try:
-            from tools.vision_tools import vision_analyze_tool
+            from hermes_agent.tools.vision import vision_analyze_tool
 
             result_json = asyncio.run(
                 vision_analyze_tool(image_url=vision_source, user_prompt=analysis_prompt)
@@ -6560,7 +6563,7 @@ class AIAgent:
         """Return the cached AnthropicTransport instance (lazy singleton)."""
         t = getattr(self, "_anthropic_transport", None)
         if t is None:
-            from agent.transports import get_transport
+            from hermes_agent.providers import get_transport
             t = get_transport("anthropic_messages")
             self._anthropic_transport = t
         return t
@@ -6569,7 +6572,7 @@ class AIAgent:
         """Return the cached ResponsesApiTransport instance (lazy singleton)."""
         t = getattr(self, "_codex_transport", None)
         if t is None:
-            from agent.transports import get_transport
+            from hermes_agent.providers import get_transport
             t = get_transport("codex_responses")
             self._codex_transport = t
         return t
@@ -6578,7 +6581,7 @@ class AIAgent:
         """Return the cached ChatCompletionsTransport instance (lazy singleton)."""
         t = getattr(self, "_chat_completions_transport", None)
         if t is None:
-            from agent.transports import get_transport
+            from hermes_agent.providers import get_transport
             t = get_transport("chat_completions")
             self._chat_completions_transport = t
         return t
@@ -6587,7 +6590,7 @@ class AIAgent:
         """Return the cached BedrockTransport instance (lazy singleton)."""
         t = getattr(self, "_bedrock_transport", None)
         if t is None:
-            from agent.transports import get_transport
+            from hermes_agent.providers import get_transport
             t = get_transport("bedrock_converse")
             self._bedrock_transport = t
         return t
@@ -6792,7 +6795,7 @@ class AIAgent:
         # Temperature: _fixed_temperature_for_model may return OMIT_TEMPERATURE
         # sentinel (temperature omitted entirely), a numeric override, or None.
         try:
-            from agent.auxiliary_client import _fixed_temperature_for_model, OMIT_TEMPERATURE
+            from hermes_agent.providers.auxiliary import _fixed_temperature_for_model, OMIT_TEMPERATURE
             _ft = _fixed_temperature_for_model(self.model, self.base_url)
             _omit_temp = _ft is OMIT_TEMPERATURE
             _fixed_temp = _ft if not _omit_temp else None
@@ -6819,7 +6822,7 @@ class AIAgent:
         _ant_max = None
         if (_is_or or _is_nous) and "claude" in (self.model or "").lower():
             try:
-                from agent.anthropic_adapter import _get_anthropic_max_output
+                from hermes_agent.providers.anthropic_adapter import _get_anthropic_max_output
                 _ant_max = _get_anthropic_max_output(self.model)
             except Exception:
                 pass  # fail open — let the proxy pick its default
@@ -6885,7 +6888,7 @@ class AIAgent:
             or base_url_host_matches(self._base_url_lower, "api.githubcopilot.com")
         ):
             try:
-                from hermes_cli.models import github_model_reasoning_efforts
+                from hermes_agent.cli.models.models import github_model_reasoning_efforts
 
                 return bool(github_model_reasoning_efforts(self.model))
             except Exception:
@@ -6909,7 +6912,7 @@ class AIAgent:
     def _github_models_reasoning_extra_body(self) -> dict | None:
         """Format reasoning payload for GitHub Models/OpenAI-compatible routes."""
         try:
-            from hermes_cli.models import github_model_reasoning_efforts
+            from hermes_agent.cli.models.models import github_model_reasoning_efforts
         except Exception:
             return None
 
@@ -7188,7 +7191,7 @@ class AIAgent:
 
             # Use auxiliary client for the flush call when available --
             # it's cheaper and avoids Codex Responses API incompatibility.
-            from agent.auxiliary_client import (
+            from hermes_agent.providers.auxiliary import (
                 call_llm as _call_llm,
                 _fixed_temperature_for_model,
                 OMIT_TEMPERATURE,
@@ -7205,12 +7208,15 @@ class AIAgent:
                 _flush_temperature = _fixed_temp
             else:
                 _flush_temperature = 0.3
+            _flush_llm_kwargs: dict = {}
+            if _flush_temperature is not None:
+                _flush_llm_kwargs["temperature"] = _flush_temperature
             try:
                 response = _call_llm(
                     task="flush_memories",
                     messages=api_messages,
                     tools=[memory_tool_def],
-                    temperature=_flush_temperature,
+                    **_flush_llm_kwargs,
                     max_tokens=5120,
                     # timeout resolved from auxiliary.flush_memories.timeout config
                 )
@@ -7248,7 +7254,7 @@ class AIAgent:
                 }
                 if _flush_temperature is not None:
                     api_kwargs["temperature"] = _flush_temperature
-                from agent.auxiliary_client import _get_task_timeout
+                from hermes_agent.providers.auxiliary import _get_task_timeout
                 response = self._ensure_primary_openai_client(reason="flush_memories").chat.completions.create(
                     **api_kwargs, timeout=_get_task_timeout("flush_memories")
                 )
@@ -7285,7 +7291,7 @@ class AIAgent:
                     try:
                         args = json.loads(tc.function.arguments)
                         flush_target = args.get("target", "memory")
-                        from tools.memory_tool import memory_tool as _memory_tool
+                        from hermes_agent.tools.memory import memory_tool as _memory_tool
                         _memory_tool(
                             action=args.get("action"),
                             target=flush_target,
@@ -7399,7 +7405,7 @@ class AIAgent:
         # read content is summarised away — if the model re-reads the same
         # file it needs the full content, not a "file unchanged" stub.
         try:
-            from tools.file_tools import reset_file_dedup
+            from hermes_agent.tools.files.tools import reset_file_dedup
             reset_file_dedup(task_id)
         except Exception:
             pass
@@ -7440,7 +7446,7 @@ class AIAgent:
         New DELEGATE_TASK_SCHEMA fields only need to be added here to reach all
         invocation paths (concurrent, sequential, inline).
         """
-        from tools.delegate_tool import delegate_task as _delegate_task
+        from hermes_agent.tools.delegate import delegate_task as _delegate_task
         return _delegate_task(
             goal=function_args.get("goal"),
             context=function_args.get("context"),
@@ -7464,7 +7470,7 @@ class AIAgent:
         # Check plugin hooks for a block directive before executing anything.
         block_message: Optional[str] = None
         try:
-            from hermes_cli.plugins import get_pre_tool_call_block_message
+            from hermes_agent.cli.plugins import get_pre_tool_call_block_message
             block_message = get_pre_tool_call_block_message(
                 function_name, function_args, task_id=effective_task_id or "",
             )
@@ -7474,7 +7480,7 @@ class AIAgent:
             return json.dumps({"error": block_message}, ensure_ascii=False)
 
         if function_name == "todo":
-            from tools.todo_tool import todo_tool as _todo_tool
+            from hermes_agent.tools.todo import todo_tool as _todo_tool
             return _todo_tool(
                 todos=function_args.get("todos"),
                 merge=function_args.get("merge", False),
@@ -7483,7 +7489,7 @@ class AIAgent:
         elif function_name == "session_search":
             if not self._session_db:
                 return json.dumps({"success": False, "error": "Session database not available."})
-            from tools.session_search_tool import session_search as _session_search
+            from hermes_agent.tools.session_search import session_search as _session_search
             return _session_search(
                 query=function_args.get("query", ""),
                 role_filter=function_args.get("role_filter"),
@@ -7493,7 +7499,7 @@ class AIAgent:
             )
         elif function_name == "memory":
             target = function_args.get("target", "memory")
-            from tools.memory_tool import memory_tool as _memory_tool
+            from hermes_agent.tools.memory import memory_tool as _memory_tool
             result = _memory_tool(
                 action=function_args.get("action"),
                 target=target,
@@ -7515,7 +7521,7 @@ class AIAgent:
         elif self._memory_manager and self._memory_manager.has_tool(function_name):
             return self._memory_manager.handle_tool_call(function_name, function_args)
         elif function_name == "clarify":
-            from tools.clarify_tool import clarify_tool as _clarify_tool
+            from hermes_agent.tools.clarify import clarify_tool as _clarify_tool
             return _clarify_tool(
                 question=function_args.get("question", ""),
                 choices=function_args.get("choices"),
@@ -7678,7 +7684,7 @@ class AIAgent:
             # The callback is thread-local; the main thread's callback
             # is invisible to worker threads.
             try:
-                from tools.environments.base import set_activity_callback
+                from hermes_agent.backends.base import set_activity_callback
                 set_activity_callback(self._touch_activity)
             except Exception:
                 pass
@@ -7893,7 +7899,7 @@ class AIAgent:
             # Check plugin hooks for a block directive before executing.
             _block_msg: Optional[str] = None
             try:
-                from hermes_cli.plugins import get_pre_tool_call_block_message
+                from hermes_agent.cli.plugins import get_pre_tool_call_block_message
                 _block_msg = get_pre_tool_call_block_message(
                     function_name, function_args, task_id=effective_task_id or "",
                 )
@@ -7929,7 +7935,7 @@ class AIAgent:
             # the agent while a command is running.
             if _block_msg is None:
                 try:
-                    from tools.environments.base import set_activity_callback
+                    from hermes_agent.backends.base import set_activity_callback
                     set_activity_callback(self._touch_activity)
                 except Exception:
                     pass
@@ -7978,7 +7984,7 @@ class AIAgent:
                 function_result = json.dumps({"error": _block_msg}, ensure_ascii=False)
                 tool_duration = 0.0
             elif function_name == "todo":
-                from tools.todo_tool import todo_tool as _todo_tool
+                from hermes_agent.tools.todo import todo_tool as _todo_tool
                 function_result = _todo_tool(
                     todos=function_args.get("todos"),
                     merge=function_args.get("merge", False),
@@ -7991,7 +7997,7 @@ class AIAgent:
                 if not self._session_db:
                     function_result = json.dumps({"success": False, "error": "Session database not available."})
                 else:
-                    from tools.session_search_tool import session_search as _session_search
+                    from hermes_agent.tools.session_search import session_search as _session_search
                     function_result = _session_search(
                         query=function_args.get("query", ""),
                         role_filter=function_args.get("role_filter"),
@@ -8004,7 +8010,7 @@ class AIAgent:
                     self._vprint(f"  {_get_cute_tool_message_impl('session_search', function_args, tool_duration, result=function_result)}")
             elif function_name == "memory":
                 target = function_args.get("target", "memory")
-                from tools.memory_tool import memory_tool as _memory_tool
+                from hermes_agent.tools.memory import memory_tool as _memory_tool
                 function_result = _memory_tool(
                     action=function_args.get("action"),
                     target=target,
@@ -8026,7 +8032,7 @@ class AIAgent:
                 if self._should_emit_quiet_tool_messages():
                     self._vprint(f"  {_get_cute_tool_message_impl('memory', function_args, tool_duration, result=function_result)}")
             elif function_name == "clarify":
-                from tools.clarify_tool import clarify_tool as _clarify_tool
+                from hermes_agent.tools.clarify import clarify_tool as _clarify_tool
                 function_result = _clarify_tool(
                     question=function_args.get("question", ""),
                     choices=function_args.get("choices"),
@@ -8281,7 +8287,7 @@ class AIAgent:
 
             summary_extra_body = {}
             try:
-                from agent.auxiliary_client import _fixed_temperature_for_model, OMIT_TEMPERATURE as _OMIT_TEMP
+                from hermes_agent.providers.auxiliary import _fixed_temperature_for_model, OMIT_TEMPERATURE as _OMIT_TEMP
             except Exception:
                 _fixed_temperature_for_model = None
                 _OMIT_TEMP = None
@@ -8418,9 +8424,9 @@ class AIAgent:
         self,
         user_message: str,
         system_message: str = None,
-        conversation_history: List[Dict[str, Any]] = None,
+        conversation_history: List[Dict[str, Any]] | None = None,
         task_id: str = None,
-        stream_callback: Optional[callable] = None,
+        stream_callback: Optional[Callable[..., Any]] = None,
         persist_user_message: Optional[str] = None,
     ) -> Dict[str, Any]:
         """
@@ -8448,7 +8454,7 @@ class AIAgent:
 
         # Tag all log records on this thread with the session ID so
         # ``hermes logs --session <id>`` can filter a single conversation.
-        from hermes_logging import set_session_context
+        from hermes_agent.logging import set_session_context
         set_session_context(self.session_id)
 
         # If the previous turn activated fallback, restore the primary
@@ -8610,7 +8616,7 @@ class AIAgent:
                 # continuation).  Plugins can use this to initialise
                 # session-scoped state (e.g. warm a memory cache).
                 try:
-                    from hermes_cli.plugins import invoke_hook as _invoke_hook
+                    from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
                     _invoke_hook(
                         "on_session_start",
                         session_id=self.session_id,
@@ -8711,7 +8717,7 @@ class AIAgent:
         # All injected context is ephemeral (not persisted to session DB).
         _plugin_user_context = ""
         try:
-            from hermes_cli.plugins import invoke_hook as _invoke_hook
+            from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
             _pre_results = _invoke_hook(
                 "pre_llm_call",
                 session_id=self.session_id,
@@ -9085,7 +9091,7 @@ class AIAgent:
                 # deepens the rate limit hole.
                 if self.provider == "nous":
                     try:
-                        from agent.nous_rate_guard import (
+                        from hermes_agent.providers.nous_rate_guard import (
                             nous_rate_limit_remaining,
                             format_remaining as _fmt_nous_remaining,
                         )
@@ -9134,7 +9140,7 @@ class AIAgent:
                         api_kwargs = self._get_codex_transport().preflight_kwargs(api_kwargs, allow_stream=False)
 
                     try:
-                        from hermes_cli.plugins import invoke_hook as _invoke_hook
+                        from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
                         _invoke_hook(
                             "pre_api_request",
                             task_id=effective_task_id,
@@ -9759,7 +9765,7 @@ class AIAgent:
                     # resume hitting Nous.
                     if self.provider == "nous":
                         try:
-                            from agent.nous_rate_guard import clear_nous_rate_limit
+                            from hermes_agent.providers.nous_rate_guard import clear_nous_rate_limit
                             clear_nous_rate_limit()
                         except Exception:
                             pass
@@ -10007,7 +10013,7 @@ class AIAgent:
                         and not anthropic_auth_retry_attempted
                     ):
                         anthropic_auth_retry_attempted = True
-                        from agent.anthropic_adapter import _is_oauth_token
+                        from hermes_agent.providers.anthropic_adapter import _is_oauth_token
                         if self._try_refresh_anthropic_client_credentials():
                             print(f"{self.log_prefix}🔐 Anthropic credentials refreshed after 401. Retrying request...")
                             continue
@@ -10016,9 +10022,9 @@ class AIAgent:
                         auth_method = "Bearer (OAuth/setup-token)" if _is_oauth_token(key) else "x-api-key (API key)"
                         print(f"{self.log_prefix}🔐 Anthropic 401 — authentication failed.")
                         print(f"{self.log_prefix}   Auth method: {auth_method}")
-                        print(f"{self.log_prefix}   Token prefix: {key[:12]}..." if key and len(key) > 12 else f"{self.log_prefix}   Token: (empty or short)")
+                        print(f"{self.log_prefix}   Token prefix: {str(key)[:12]}..." if key and len(str(key)) > 12 else f"{self.log_prefix}   Token: (empty or short)")
                         print(f"{self.log_prefix}   Troubleshooting:")
-                        from hermes_constants import display_hermes_home as _dhh_fn
+                        from hermes_agent.constants import display_hermes_home as _dhh_fn
                         _dhh = _dhh_fn()
                         print(f"{self.log_prefix}     • Check ANTHROPIC_TOKEN in {_dhh}/.env for Hermes-managed OAuth/setup tokens")
                         print(f"{self.log_prefix}     • Check ANTHROPIC_API_KEY in {_dhh}/.env for API keys or legacy token values")
@@ -10227,7 +10233,7 @@ class AIAgent:
                         and not recovered_with_pool
                     ):
                         try:
-                            from agent.nous_rate_guard import record_nous_rate_limit
+                            from hermes_agent.providers.nous_rate_guard import record_nous_rate_limit
                             _err_resp = getattr(api_error, "response", None)
                             _err_hdrs = (
                                 getattr(_err_resp, "headers", None)
@@ -10770,7 +10776,7 @@ class AIAgent:
                         assistant_message.content = str(raw)
 
                 try:
-                    from hermes_cli.plugins import invoke_hook as _invoke_hook
+                    from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
                     _assistant_tool_calls = getattr(assistant_message, "tool_calls", None) or []
                     _assistant_text = assistant_message.content or ""
                     _invoke_hook(
@@ -11416,7 +11422,7 @@ class AIAgent:
                         messages.append(assistant_msg)
 
                         if reasoning_text:
-                            reasoning_preview = reasoning_text[:500] + "..." if len(reasoning_text) > 500 else reasoning_text
+                            reasoning_preview = str(reasoning_text)[:500] + "..." if len(str(reasoning_text)) > 500 else reasoning_text
                             logger.warning(
                                 "Reasoning-only response (no visible content) "
                                 "after exhausting retries and fallback. "
@@ -11636,7 +11642,7 @@ class AIAgent:
         # to an external memory system).
         if final_response and not interrupted:
             try:
-                from hermes_cli.plugins import invoke_hook as _invoke_hook
+                from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
                 _invoke_hook(
                     "post_llm_call",
                     session_id=self.session_id,
@@ -11741,7 +11747,7 @@ class AIAgent:
         # Fired at the very end of every run_conversation call.
         # Plugins can use this for cleanup, flushing buffers, etc.
         try:
-            from hermes_cli.plugins import invoke_hook as _invoke_hook
+            from hermes_agent.cli.plugins import invoke_hook as _invoke_hook
             _invoke_hook(
                 "on_session_end",
                 session_id=self.session_id,
@@ -11755,7 +11761,7 @@ class AIAgent:
 
         return result
 
-    def chat(self, message: str, stream_callback: Optional[callable] = None) -> str:
+    def chat(self, message: str, stream_callback: Optional[Callable[..., Any]] = None) -> str:
         """
         Simple chat interface that returns just the final response.
 
@@ -11811,8 +11817,8 @@ def main(
     
     # Handle tool listing
     if list_tools:
-        from model_tools import get_all_tool_names, get_available_toolsets
-        from toolsets import get_all_toolsets, get_toolset_info
+        from hermes_agent.tools.dispatch import get_all_tool_names, get_available_toolsets
+        from hermes_agent.tools.toolsets import get_all_toolsets, get_toolset_info
         
         print("📋 Available Tools & Toolsets:")
         print("-" * 50)

hermes_agent/agent/memory/manager.py

@@ -33,8 +33,8 @@ import logging
 import re
 from typing import Any, Dict, List, Optional
 
-from agent.memory_provider import MemoryProvider
-from tools.registry import tool_error
+from hermes_agent.agent.memory.provider import MemoryProvider
+from hermes_agent.tools.registry import tool_error
 
 logger = logging.getLogger(__name__)
 
@@ -361,7 +361,7 @@ class MemoryManager:
         ``get_hermes_home()`` themselves.
         """
         if "hermes_home" not in kwargs:
-            from hermes_constants import get_hermes_home
+            from hermes_agent.constants import get_hermes_home
             kwargs["hermes_home"] = str(get_hermes_home())
         for provider in self._providers:
             try:

hermes_agent/agent/prompt_builder.py

@@ -12,10 +12,10 @@ import threading
 from collections import OrderedDict
 from pathlib import Path
 
-from hermes_constants import get_hermes_home, get_skills_dir, is_wsl
+from hermes_agent.constants import get_hermes_home, get_skills_dir, is_wsl
 from typing import Optional
 
-from agent.skill_utils import (
+from hermes_agent.agent.skill_utils import (
     extract_skill_conditions,
     extract_skill_description,
     get_all_skills_dirs,
@@ -24,7 +24,7 @@ from agent.skill_utils import (
     parse_frontmatter,
     skill_matches_platform,
 )
-from utils import atomic_json_write
+from hermes_agent.utils import atomic_json_write
 
 logger = logging.getLogger(__name__)
 
@@ -619,7 +619,7 @@ def build_skills_system_prompt(
     # ── Layer 1: in-process LRU cache ─────────────────────────────────
     # Include the resolved platform so per-platform disabled-skill lists
     # produce distinct cache entries (gateway serves multiple platforms).
-    from gateway.session_context import get_session_env
+    from hermes_agent.gateway.session_context import get_session_env
     _platform_hint = (
         os.environ.get("HERMES_PLATFORM")
         or get_session_env("HERMES_SESSION_PLATFORM")
@@ -824,8 +824,8 @@ def build_skills_system_prompt(
 def build_nous_subscription_prompt(valid_tool_names: "set[str] | None" = None) -> str:
     """Build a compact Nous subscription capability block for the system prompt."""
     try:
-        from hermes_cli.nous_subscription import get_nous_subscription_features
-        from tools.tool_backend_helpers import managed_nous_tools_enabled
+        from hermes_agent.cli.nous_subscription import get_nous_subscription_features
+        from hermes_agent.tools.backend_helpers import managed_nous_tools_enabled
     except Exception as exc:
         logger.debug("Failed to import Nous subscription helper: %s", exc)
         return ""
@@ -911,7 +911,7 @@ def load_soul_md() -> Optional[str]:
     ``skip_soul=True`` so SOUL.md isn't injected twice.
     """
     try:
-        from hermes_cli.config import ensure_hermes_home
+        from hermes_agent.cli.config import ensure_hermes_home
         ensure_hermes_home()
     except Exception as e:
         logger.debug("Could not ensure HERMES_HOME before loading SOUL.md: %s", e)

hermes_agent/agent/shell_hooks.py

@@ -75,7 +75,7 @@ try:
 except ImportError:  # pragma: no cover
     fcntl = None  # type: ignore[assignment]
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 logger = logging.getLogger(__name__)
 
@@ -177,7 +177,7 @@ def register_from_config(
     registered: List[ShellHookSpec] = []
 
     # Import lazily — avoids circular imports at module-load time.
-    from hermes_cli.plugins import get_plugin_manager
+    from hermes_agent.cli.plugins import get_plugin_manager
 
     manager = get_plugin_manager()
 
@@ -243,7 +243,7 @@ def _parse_hooks_block(hooks_cfg: Any) -> List[ShellHookSpec]:
     Malformed entries warn-and-skip — we never raise from config parsing
     because a broken hook must not crash the agent.
     """
-    from hermes_cli.plugins import VALID_HOOKS
+    from hermes_agent.cli.plugins import VALID_HOOKS
 
     if not isinstance(hooks_cfg, dict):
         return []

hermes_agent/agent/skill_commands.py

@@ -13,7 +13,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Any, Dict, Optional
 
-from hermes_constants import display_hermes_home
+from hermes_agent.constants import display_hermes_home
 
 logger = logging.getLogger(__name__)
 
@@ -39,7 +39,7 @@ _INLINE_SHELL_MAX_OUTPUT = 4000
 def _load_skills_config() -> dict:
     """Load the ``skills`` section of config.yaml (best-effort)."""
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
 
         cfg = load_config() or {}
         skills_cfg = cfg.get("skills")
@@ -156,7 +156,7 @@ def _load_skill_payload(skill_identifier: str, task_id: str | None = None) -> tu
         return None
 
     try:
-        from tools.skills_tool import SKILLS_DIR, skill_view
+        from hermes_agent.tools.skills.tool import SKILLS_DIR, skill_view
 
         identifier_path = Path(raw_identifier).expanduser()
         if identifier_path.is_absolute():
@@ -202,7 +202,7 @@ def _inject_skill_config(loaded_skill: dict[str, Any], parts: list[str]) -> None
     without needing to read config.yaml itself.
     """
     try:
-        from agent.skill_utils import (
+        from hermes_agent.agent.skill_utils import (
             extract_skill_config_vars,
             parse_frontmatter,
             resolve_skill_config_values,
@@ -241,7 +241,7 @@ def _build_skill_message(
     session_id: str | None = None,
 ) -> str:
     """Format a loaded skill into a user/system message payload."""
-    from tools.skills_tool import SKILLS_DIR
+    from hermes_agent.tools.skills.tool import SKILLS_DIR
 
     content = str(loaded_skill.get("content") or "")
 
@@ -344,8 +344,8 @@ def scan_skill_commands() -> Dict[str, Dict[str, Any]]:
     global _skill_commands
     _skill_commands = {}
     try:
-        from tools.skills_tool import SKILLS_DIR, _parse_frontmatter, skill_matches_platform, _get_disabled_skill_names
-        from agent.skill_utils import get_external_skills_dirs
+        from hermes_agent.tools.skills.tool import SKILLS_DIR, _parse_frontmatter, skill_matches_platform, _get_disabled_skill_names
+        from hermes_agent.agent.skill_utils import get_external_skills_dirs
         disabled = _get_disabled_skill_names()
         seen_names: set = set()
 

hermes_agent/agent/skill_utils.py

@@ -12,7 +12,7 @@ import sys
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Set, Tuple
 
-from hermes_constants import get_config_path, get_skills_dir
+from hermes_agent.constants import get_config_path, get_skills_dir
 
 logger = logging.getLogger(__name__)
 
@@ -145,7 +145,7 @@ def get_disabled_skill_names(platform: str | None = None) -> Set[str]:
     if not isinstance(skills_cfg, dict):
         return set()
 
-    from gateway.session_context import get_session_env
+    from hermes_agent.gateway.session_context import get_session_env
     resolved_platform = (
         platform
         or os.getenv("HERMES_PLATFORM")
@@ -455,7 +455,8 @@ def parse_qualified_name(name: str) -> Tuple[Optional[str], str]:
     """
     if ":" not in name:
         return None, name
-    return tuple(name.split(":", 1))  # type: ignore[return-value]
+    ns, bare = name.split(":", 1)
+    return ns, bare
 
 
 def is_valid_namespace(candidate: Optional[str]) -> bool:

hermes_agent/agent/subdirectory_hints.py

@@ -19,7 +19,7 @@ import shlex
 from pathlib import Path
 from typing import Dict, Any, Optional, Set
 
-from agent.prompt_builder import _scan_context_content
+from hermes_agent.agent.prompt_builder import _scan_context_content
 
 logger = logging.getLogger(__name__)
 

hermes_agent/agent/title_generator.py

@@ -8,7 +8,7 @@ import logging
 import threading
 from typing import Optional
 
-from agent.auxiliary_client import call_llm
+from hermes_agent.providers.auxiliary import call_llm
 
 logger = logging.getLogger(__name__)
 

hermes_agent/backends/__init__.py

@@ -8,6 +8,6 @@ The terminal_tool.py factory (_create_environment) selects the backend
 based on the TERMINAL_ENV configuration.
 """
 
-from tools.environments.base import BaseEnvironment
+from hermes_agent.backends.base import BaseEnvironment
 
 __all__ = ["BaseEnvironment"]

hermes_agent/backends/base.py

@@ -20,8 +20,8 @@ from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import IO, Callable, Protocol
 
-from hermes_constants import get_hermes_home
-from tools.interrupt import is_interrupted
+from hermes_agent.constants import get_hermes_home
+from hermes_agent.tools.interrupt import is_interrupted
 
 logger = logging.getLogger(__name__)
 
@@ -245,7 +245,7 @@ class _ThreadedProcessHandle:
             except Exception:
                 pass
 
-    def wait(self, timeout: float | None = None) -> int:
+    def wait(self, timeout: float | None = None) -> int | None:
         self._done.wait(timeout=timeout)
         return self._returncode
 
@@ -710,7 +710,7 @@ class BaseEnvironment(ABC):
         # server, `yes > /dev/null`, etc.), leaking the subshell forever.
         # Rewriting to `A && { B & }` runs B as a plain background in the
         # current shell — no subshell wait.
-        from tools.terminal_tool import _rewrite_compound_background
+        from hermes_agent.tools.terminal import _rewrite_compound_background
         exec_command = _rewrite_compound_background(exec_command)
         effective_timeout = timeout or self.timeout
         effective_cwd = cwd or self.cwd
@@ -755,9 +755,9 @@ class BaseEnvironment(ABC):
         except Exception:
             pass
 
-    def _prepare_command(self, command: str) -> tuple[str, str | None]:
+    def _prepare_command(self, command: str) -> tuple[str | None, str | None]:
         """Transform sudo commands if SUDO_PASSWORD is available."""
-        from tools.terminal_tool import _transform_sudo_command
+        from hermes_agent.tools.terminal import _transform_sudo_command
 
         return _transform_sudo_command(command)
 

hermes_agent/backends/daytona.py

@@ -12,11 +12,11 @@ import shlex
 import threading
 from pathlib import Path
 
-from tools.environments.base import (
+from hermes_agent.backends.base import (
     BaseEnvironment,
     _ThreadedProcessHandle,
 )
-from tools.environments.file_sync import (
+from hermes_agent.backends.file_sync import (
     FileSyncManager,
     iter_sync_files,
     quoted_mkdir_command,

hermes_agent/backends/docker.py

@@ -14,8 +14,8 @@ import sys
 import uuid
 from typing import Optional
 
-from tools.environments.base import BaseEnvironment, _popen_bash
-from tools.environments.local import _HERMES_PROVIDER_ENV_BLOCKLIST
+from hermes_agent.backends.base import BaseEnvironment, _popen_bash
+from hermes_agent.backends.local import _HERMES_PROVIDER_ENV_BLOCKLIST
 
 logger = logging.getLogger(__name__)
 
@@ -91,7 +91,7 @@ def _normalize_env_dict(env: dict | None) -> dict[str, str]:
 def _load_hermes_env_vars() -> dict[str, str]:
     """Load ~/.hermes/.env values without failing Docker command execution."""
     try:
-        from hermes_cli.config import load_env
+        from hermes_agent.cli.config import load_env
 
         return load_env() or {}
     except Exception:
@@ -298,7 +298,7 @@ class DockerEnvironment(BaseEnvironment):
         # Persistent workspace via bind mounts from a configurable host directory
         # (TERMINAL_SANDBOX_DIR, default ~/.hermes/sandboxes/). Non-persistent
         # mode uses tmpfs (ephemeral, fast, gone on cleanup).
-        from tools.environments.base import get_sandbox_dir
+        from hermes_agent.backends.base import get_sandbox_dir
 
         # User-configured volume mounts (from config.yaml docker_volumes)
         volume_args = []
@@ -362,7 +362,7 @@ class DockerEnvironment(BaseEnvironment):
         # Mount credential files (OAuth tokens, etc.) declared by skills.
         # Read-only so the container can authenticate but not modify host creds.
         try:
-            from tools.credential_files import (
+            from hermes_agent.tools.credential_files import (
                 get_credential_file_mounts,
                 get_skills_directory_mount,
                 get_cache_directory_mounts,
@@ -464,7 +464,7 @@ class DockerEnvironment(BaseEnvironment):
         explicit_forward_keys = set(self._forward_env)
         passthrough_keys: set[str] = set()
         try:
-            from tools.env_passthrough import get_all_passthrough
+            from hermes_agent.tools.env_passthrough import get_all_passthrough
             passthrough_keys = set(get_all_passthrough())
         except Exception:
             pass

hermes_agent/backends/file_sync.py

@@ -24,8 +24,8 @@ except ImportError:
 from pathlib import Path
 from typing import Callable
 
-from hermes_constants import get_hermes_home
-from tools.environments.base import _file_mtime_key
+from hermes_agent.constants import get_hermes_home
+from hermes_agent.backends.base import _file_mtime_key
 
 logger = logging.getLogger(__name__)
 
@@ -50,7 +50,7 @@ def iter_sync_files(container_base: str = "/root/.hermes") -> list[tuple[str, st
     """
     # Late import: credential_files imports agent modules that create
     # circular dependencies if loaded at file_sync module level.
-    from tools.credential_files import (
+    from hermes_agent.tools.credential_files import (
         get_credential_file_mounts,
         iter_cache_files,
         iter_skills_files,

hermes_agent/backends/local.py

@@ -7,7 +7,7 @@ import signal
 import subprocess
 import tempfile
 
-from tools.environments.base import BaseEnvironment, _pipe_stdin
+from hermes_agent.backends.base import BaseEnvironment, _pipe_stdin
 
 _IS_WINDOWS = platform.system() == "Windows"
 
@@ -21,7 +21,7 @@ def _build_provider_env_blocklist() -> frozenset:
     blocked: set[str] = set()
 
     try:
-        from hermes_cli.auth import PROVIDER_REGISTRY
+        from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
         for pconfig in PROVIDER_REGISTRY.values():
             blocked.update(pconfig.api_key_env_vars)
             if pconfig.base_url_env_var:
@@ -30,7 +30,7 @@ def _build_provider_env_blocklist() -> frozenset:
         pass
 
     try:
-        from hermes_cli.config import OPTIONAL_ENV_VARS
+        from hermes_agent.cli.config import OPTIONAL_ENV_VARS
         for name, metadata in OPTIONAL_ENV_VARS.items():
             category = metadata.get("category")
             if category in {"tool", "messaging"}:
@@ -110,7 +110,7 @@ _HERMES_PROVIDER_ENV_BLOCKLIST = _build_provider_env_blocklist()
 def _sanitize_subprocess_env(base_env: dict | None, extra_env: dict | None = None) -> dict:
     """Filter Hermes-managed secrets from a subprocess environment."""
     try:
-        from tools.env_passthrough import is_env_passthrough as _is_passthrough
+        from hermes_agent.tools.env_passthrough import is_env_passthrough as _is_passthrough
     except Exception:
         _is_passthrough = lambda _: False  # noqa: E731
 
@@ -130,7 +130,7 @@ def _sanitize_subprocess_env(base_env: dict | None, extra_env: dict | None = Non
             sanitized[key] = value
 
     # Per-profile HOME isolation for background processes (same as _make_run_env).
-    from hermes_constants import get_subprocess_home
+    from hermes_agent.constants import get_subprocess_home
     _profile_home = get_subprocess_home()
     if _profile_home:
         sanitized["HOME"] = _profile_home
@@ -186,7 +186,7 @@ _SANE_PATH = (
 def _make_run_env(env: dict) -> dict:
     """Build a run environment with a sane PATH and provider-var stripping."""
     try:
-        from tools.env_passthrough import is_env_passthrough as _is_passthrough
+        from hermes_agent.tools.env_passthrough import is_env_passthrough as _is_passthrough
     except Exception:
         _is_passthrough = lambda _: False  # noqa: E731
 
@@ -205,7 +205,7 @@ def _make_run_env(env: dict) -> dict:
     # Per-profile HOME isolation: redirect system tool configs (git, ssh, gh,
     # npm …) into {HERMES_HOME}/home/ when that directory exists.  Only the
     # subprocess sees the override — the Python process keeps the real HOME.
-    from hermes_constants import get_subprocess_home
+    from hermes_agent.constants import get_subprocess_home
     _profile_home = get_subprocess_home()
     if _profile_home:
         run_env["HOME"] = _profile_home
@@ -220,7 +220,7 @@ def _read_terminal_shell_init_config() -> tuple[list[str], bool]:
     execution never breaks because the config file is unreadable.
     """
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
 
         cfg = load_config() or {}
         terminal_cfg = cfg.get("terminal") or {}

hermes_agent/backends/managed_modal.py

@@ -10,12 +10,12 @@ import uuid
 from dataclasses import dataclass
 from typing import Any, Dict, Optional
 
-from tools.environments.modal_utils import (
+from hermes_agent.backends.modal_utils import (
     BaseModalExecutionEnvironment,
     ModalExecStart,
     PreparedModalExec,
 )
-from tools.managed_tool_gateway import resolve_managed_tool_gateway
+from hermes_agent.tools.managed_gateway import resolve_managed_tool_gateway
 
 logger = logging.getLogger(__name__)
 
@@ -214,7 +214,7 @@ class ManagedModalEnvironment(BaseModalExecutionEnvironment):
     def _guard_unsupported_credential_passthrough(self) -> None:
         """Managed Modal does not sync or mount host credential files."""
         try:
-            from tools.credential_files import get_credential_file_mounts
+            from hermes_agent.tools.credential_files import get_credential_file_mounts
         except Exception:
             return
 

hermes_agent/backends/modal.py

@@ -14,14 +14,14 @@ import threading
 from pathlib import Path
 from typing import Any, Optional
 
-from hermes_constants import get_hermes_home
-from tools.environments.base import (
+from hermes_agent.constants import get_hermes_home
+from hermes_agent.backends.base import (
     BaseEnvironment,
     _ThreadedProcessHandle,
     _load_json_store,
     _save_json_store,
 )
-from tools.environments.file_sync import (
+from hermes_agent.backends.file_sync import (
     FileSyncManager,
     iter_sync_files,
     quoted_mkdir_command,
@@ -187,7 +187,7 @@ class ModalEnvironment(BaseEnvironment):
 
         cred_mounts = []
         try:
-            from tools.credential_files import (
+            from hermes_agent.tools.credential_files import (
                 get_credential_file_mounts,
                 iter_skills_files,
                 iter_cache_files,

hermes_agent/backends/modal_utils.py

@@ -20,8 +20,8 @@ from abc import abstractmethod
 from dataclasses import dataclass
 from typing import Any
 
-from tools.environments.base import BaseEnvironment
-from tools.interrupt import is_interrupted
+from hermes_agent.backends.base import BaseEnvironment
+from hermes_agent.tools.interrupt import is_interrupted
 
 
 @dataclass(frozen=True)
@@ -136,7 +136,7 @@ class BaseModalExecutionEnvironment(BaseEnvironment):
 
             # Periodic activity touch so the gateway knows we're alive
             try:
-                from tools.environments.base import touch_activity_if_due
+                from hermes_agent.backends.base import touch_activity_if_due
                 touch_activity_if_due(_activity_state, "modal command running")
             except Exception:
                 pass

hermes_agent/backends/singularity.py

@@ -14,8 +14,8 @@ import uuid
 from pathlib import Path
 from typing import Optional
 
-from hermes_constants import get_hermes_home
-from tools.environments.base import (
+from hermes_agent.constants import get_hermes_home
+from hermes_agent.backends.base import (
     BaseEnvironment,
     _load_json_store,
     _popen_bash,
@@ -75,7 +75,7 @@ def _get_scratch_dir() -> Path:
         scratch_path.mkdir(parents=True, exist_ok=True)
         return scratch_path
 
-    from tools.environments.base import get_sandbox_dir
+    from hermes_agent.backends.base import get_sandbox_dir
     sandbox = get_sandbox_dir() / "singularity"
 
     scratch = Path("/scratch")
@@ -202,7 +202,7 @@ class SingularityEnvironment(BaseEnvironment):
             cmd.append("--writable-tmpfs")
 
         try:
-            from tools.credential_files import get_credential_file_mounts, get_skills_directory_mount
+            from hermes_agent.tools.credential_files import get_credential_file_mounts, get_skills_directory_mount
             for mount_entry in get_credential_file_mounts():
                 cmd.extend(["--bind", f"{mount_entry['host_path']}:{mount_entry['container_path']}:ro"])
             for skills_mount in get_skills_directory_mount():

hermes_agent/backends/ssh.py

@@ -9,8 +9,8 @@ import subprocess
 import tempfile
 from pathlib import Path
 
-from tools.environments.base import BaseEnvironment, _popen_bash
-from tools.environments.file_sync import (
+from hermes_agent.backends.base import BaseEnvironment, _popen_bash
+from hermes_agent.backends.file_sync import (
     FileSyncManager,
     iter_sync_files,
     quoted_mkdir_command,

hermes_agent/cli/auth/auth.py

@@ -38,8 +38,8 @@ from typing import Any, Dict, List, Optional
 import httpx
 import yaml
 
-from hermes_cli.config import get_hermes_home, get_config_path, read_raw_config
-from hermes_constants import OPENROUTER_BASE_URL
+from hermes_agent.cli.config import get_hermes_home, get_config_path, read_raw_config
+from hermes_agent.constants import OPENROUTER_BASE_URL
 
 logger = logging.getLogger(__name__)
 
@@ -329,7 +329,7 @@ def get_anthropic_key() -> str:
 
         ANTHROPIC_API_KEY -> ANTHROPIC_TOKEN -> CLAUDE_CODE_OAUTH_TOKEN
     """
-    from hermes_cli.config import get_env_value
+    from hermes_agent.cli.config import get_env_value
 
     for var in PROVIDER_REGISTRY["anthropic"].api_key_env_vars:
         value = get_env_value(var) or os.getenv(var, "")
@@ -406,7 +406,7 @@ def _resolve_api_key_provider_secret(
     if provider_id == "copilot":
         # Use the dedicated copilot auth module for proper token validation
         try:
-            from hermes_cli.copilot_auth import resolve_copilot_token
+            from hermes_agent.cli.auth.copilot import resolve_copilot_token
             token, source = resolve_copilot_token()
             if token:
                 return token, source
@@ -757,16 +757,20 @@ def _save_provider_state(auth_store: Dict[str, Any], provider_id: str, state: Di
     auth_store["active_provider"] = provider_id
 
 
-def read_credential_pool(provider_id: Optional[str] = None) -> Dict[str, Any]:
-    """Return the persisted credential pool, or one provider slice."""
+def read_credential_pool() -> Dict[str, Any]:
+    """Return the entire persisted credential pool."""
     auth_store = _load_auth_store()
     pool = auth_store.get("credential_pool")
     if not isinstance(pool, dict):
         pool = {}
-    if provider_id is None:
-        return dict(pool)
-    provider_entries = pool.get(provider_id)
-    return list(provider_entries) if isinstance(provider_entries, list) else []
+    return dict(pool)
+
+
+def read_provider_credentials(provider_id: str) -> List[Dict[str, Any]]:
+    """Return credential entries for a single provider."""
+    pool = read_credential_pool()
+    entries = pool.get(provider_id)
+    return list(entries) if isinstance(entries, list) else []
 
 
 def write_credential_pool(provider_id: str, entries: List[Dict[str, Any]]) -> Path:
@@ -862,7 +866,7 @@ def is_provider_explicitly_configured(provider_id: str) -> bool:
 
     # 2. Check config.yaml model.provider
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         cfg = load_config()
         model_cfg = cfg.get("model")
         if isinstance(model_cfg, dict):
@@ -949,7 +953,7 @@ def _get_config_hint_for_unknown_provider(provider_name: str) -> str:
     and returns a human-readable diagnostic, or empty string if nothing found.
     """
     try:
-        from hermes_cli.config import validate_config_structure
+        from hermes_agent.cli.config import validate_config_structure
         issues = validate_config_structure()
         if not issues:
             return ""
@@ -1064,7 +1068,7 @@ def resolve_provider(
     # AWS Bedrock — detect via boto3 credential chain (IAM roles, SSO, env vars).
     # This runs after API-key providers so explicit keys always win.
     try:
-        from agent.bedrock_adapter import has_aws_credentials
+        from hermes_agent.providers.bedrock_adapter import has_aws_credentials
         if has_aws_credentials():
             return "bedrock"
     except ImportError:
@@ -1327,7 +1331,7 @@ def resolve_gemini_oauth_runtime_credentials(
 ) -> Dict[str, Any]:
     """Resolve runtime OAuth creds for google-gemini-cli."""
     try:
-        from agent.google_oauth import (
+        from hermes_agent.providers.google_oauth import (
             GoogleOAuthError,
             _credentials_path,
             get_valid_access_token,
@@ -1366,7 +1370,7 @@ def resolve_gemini_oauth_runtime_credentials(
 def get_gemini_oauth_auth_status() -> Dict[str, Any]:
     """Return a status dict for `hermes auth list` / `hermes status`."""
     try:
-        from agent.google_oauth import _credentials_path, load_credentials
+        from hermes_agent.providers.google_oauth import _credentials_path, load_credentials
     except ImportError:
         return {"logged_in": False, "error": "agent.google_oauth unavailable"}
     auth_path = _credentials_path()
@@ -2155,7 +2159,7 @@ def persist_nous_credentials(
     Returns the upserted :class:`PooledCredential` entry (or ``None`` if
     seeding somehow produced no match — shouldn't happen).
     """
-    from agent.credential_pool import load_pool
+    from hermes_agent.providers.credential_pool import load_pool
 
     state = dict(creds)
     if label and str(label).strip():
@@ -2436,7 +2440,7 @@ def get_nous_auth_status() -> Dict[str, Any]:
     # Check credential pool first — the dashboard device-code flow saves
     # here but may not have written to the auth store yet.
     try:
-        from agent.credential_pool import load_pool
+        from hermes_agent.providers.credential_pool import load_pool
         pool = load_pool("nous")
         if pool and pool.has_credentials():
             entry = pool.select()
@@ -2490,7 +2494,7 @@ def get_codex_auth_status() -> Dict[str, Any]:
     # Check credential pool first — this is where `hermes auth` and
     # `hermes model` store device_code tokens.
     try:
-        from agent.credential_pool import load_pool
+        from hermes_agent.providers.credential_pool import load_pool
         pool = load_pool("openai-codex")
         if pool and pool.has_credentials():
             entry = pool.select()
@@ -2611,7 +2615,7 @@ def get_auth_status(provider_id: Optional[str] = None) -> Dict[str, Any]:
     # AWS SDK providers (Bedrock) — check via boto3 credential chain
     if pconfig and pconfig.auth_type == "aws_sdk":
         try:
-            from agent.bedrock_adapter import has_aws_credentials
+            from hermes_agent.providers.bedrock_adapter import has_aws_credentials
             return {"logged_in": has_aws_credentials(), "provider": target}
         except ImportError:
             return {"logged_in": False, "provider": target, "error": "boto3 not installed"}
@@ -2800,7 +2804,7 @@ def _prompt_model_selection(
     If *unavailable_models* is provided, those models are shown grayed out
     and unselectable, with an upgrade link to *portal_url*.
     """
-    from hermes_cli.models import _format_price_per_mtok
+    from hermes_agent.cli.models.models import _format_price_per_mtok
 
     _unavailable = unavailable_models or []
 
@@ -2910,7 +2914,7 @@ def _prompt_model_selection(
             title=effective_title,
         )
         idx = menu.show()
-        from hermes_cli.curses_ui import flush_stdin
+        from hermes_agent.cli.ui.curses import flush_stdin
         flush_stdin()
         if idx is None:
             return None
@@ -2967,7 +2971,7 @@ def _save_model_choice(model_id: str) -> None:
     The model is stored in config.yaml only — NOT in .env.  This avoids
     conflicts in multi-agent setups where env vars would stomp each other.
     """
-    from hermes_cli.config import save_config, load_config
+    from hermes_agent.cli.config import save_config, load_config
 
     config = load_config()
     # Always use dict format so provider/base_url can be stored alongside
@@ -3046,7 +3050,7 @@ def _login_openai_codex(args, pconfig: ProviderConfig) -> None:
     config_path = _update_config_for_provider("openai-codex", creds.get("base_url", DEFAULT_CODEX_BASE_URL))
     print()
     print("Login successful!")
-    from hermes_constants import display_hermes_home as _dhh
+    from hermes_agent.constants import display_hermes_home as _dhh
     print(f"  Auth state: {_dhh()}/auth.json")
     print(f"  Config updated: {config_path} (model.provider=openai-codex)")
 
@@ -3383,7 +3387,7 @@ def _login_nous(args, pconfig: ProviderConfig) -> None:
                     code="invalid_token",
                 )
 
-            from hermes_cli.models import (
+            from hermes_agent.cli.models.models import (
                 _PROVIDER_MODELS, get_pricing_for_provider,
                 check_nous_free_tier, partition_nous_models_by_tier,
             )

hermes_agent/cli/auth/commands.py

@@ -9,7 +9,7 @@ import time
 from types import SimpleNamespace
 import uuid
 
-from agent.credential_pool import (
+from hermes_agent.providers.credential_pool import (
     AUTH_TYPE_API_KEY,
     AUTH_TYPE_OAUTH,
     CUSTOM_POOL_PREFIX,
@@ -27,9 +27,9 @@ from agent.credential_pool import (
     list_custom_pool_providers,
     load_pool,
 )
-import hermes_cli.auth as auth_mod
-from hermes_cli.auth import PROVIDER_REGISTRY
-from hermes_constants import OPENROUTER_BASE_URL
+import hermes_agent.cli.auth.auth as auth_mod
+from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
+from hermes_agent.constants import OPENROUTER_BASE_URL
 
 
 # Providers that support OAuth login in addition to API keys.
@@ -39,7 +39,7 @@ _OAUTH_CAPABLE_PROVIDERS = {"anthropic", "nous", "openai-codex", "qwen-oauth", "
 def _get_custom_provider_names() -> list:
     """Return list of (display_name, pool_key, provider_key) tuples."""
     try:
-        from hermes_cli.config import get_compatible_custom_providers, load_config
+        from hermes_agent.cli.config import get_compatible_custom_providers, load_config
 
         config = load_config()
     except Exception:
@@ -88,7 +88,7 @@ def _provider_base_url(provider: str) -> str:
     if provider == "openrouter":
         return OPENROUTER_BASE_URL
     if provider.startswith(CUSTOM_POOL_PREFIX):
-        from agent.credential_pool import _get_custom_provider_config
+        from hermes_agent.providers.credential_pool import _get_custom_provider_config
 
         cp_config = _get_custom_provider_config(provider)
         if cp_config:
@@ -159,7 +159,7 @@ def auth_add_command(args) -> None:
     # Matches the Codex device_code re-link pattern that predates this.
     if not provider.startswith(CUSTOM_POOL_PREFIX):
         try:
-            from hermes_cli.auth import (
+            from hermes_agent.cli.auth.auth import (
                 _load_auth_store,
                 unsuppress_credential_source,
             )
@@ -197,7 +197,7 @@ def auth_add_command(args) -> None:
         return
 
     if provider == "anthropic":
-        from agent import anthropic_adapter as anthropic_mod
+        from hermes_agent.providers import anthropic_adapter as anthropic_mod
 
         creds = anthropic_mod.run_hermes_oauth_login_pure()
         if not creds:
@@ -271,7 +271,7 @@ def auth_add_command(args) -> None:
         return
 
     if provider == "google-gemini-cli":
-        from agent.google_oauth import run_gemini_oauth_login_pure
+        from hermes_agent.providers.google_oauth import run_gemini_oauth_login_pure
 
         creds = run_gemini_oauth_login_pure()
         label = (getattr(args, "label", None) or "").strip() or (
@@ -361,8 +361,8 @@ def auth_remove_command(args) -> None:
     # handles its source-specific cleanup and we centralise suppression +
     # user-facing output here so every source behaves identically from
     # the user's perspective.
-    from agent.credential_sources import find_removal_step
-    from hermes_cli.auth import suppress_credential_source
+    from hermes_agent.providers.credential_sources import find_removal_step
+    from hermes_agent.cli.auth.auth import suppress_credential_source
 
     step = find_removal_step(provider, removed.source)
     if step is None:
@@ -396,7 +396,7 @@ def _interactive_auth() -> None:
 
     # Show AWS Bedrock credential status (not in the pool — uses boto3 chain)
     try:
-        from agent.bedrock_adapter import has_aws_credentials, resolve_aws_auth_env_var, resolve_bedrock_region
+        from hermes_agent.providers.bedrock_adapter import has_aws_credentials, resolve_aws_auth_env_var, resolve_bedrock_region
         if has_aws_credentials():
             auth_source = resolve_aws_auth_env_var() or "unknown"
             region = resolve_bedrock_region()
@@ -558,7 +558,7 @@ def _interactive_strategy() -> None:
         print("Invalid choice.")
         return
 
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
     cfg = load_config()
     pool_strategies = cfg.get("credential_pool_strategies") or {}
     if not isinstance(pool_strategies, dict):

hermes_agent/cli/auth/dingtalk.py

@@ -18,7 +18,7 @@ import os
 import sys
 import time
 import logging
-from typing import Optional, Tuple
+from typing import Any, Callable, Optional, Tuple
 
 import requests
 
@@ -108,7 +108,7 @@ def wait_for_registration_success(
     device_code: str,
     interval: int = 3,
     expires_in: int = 7200,
-    on_waiting: Optional[callable] = None,
+    on_waiting: Optional[Callable[..., Any]] = None,
 ) -> Tuple[str, str]:
     """Block until the registration succeeds or times out.
 
@@ -234,7 +234,7 @@ def dingtalk_qr_auth() -> Optional[Tuple[str, str]]:
     Returns (client_id, client_secret) on success, or None if the user
     cancelled or the flow failed.
     """
-    from hermes_cli.setup import print_info, print_success, print_warning, print_error
+    from hermes_agent.cli.setup_wizard import print_info, print_success, print_warning, print_error
 
     print()
     print_info("  Initializing DingTalk device authorization...")

hermes_agent/cli/backup.py

@@ -21,7 +21,7 @@ from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any, Dict, List, Optional
 
-from hermes_constants import get_default_hermes_root, get_hermes_home, display_hermes_home
+from hermes_agent.constants import get_default_hermes_root, get_hermes_home, display_hermes_home
 
 logger = logging.getLogger(__name__)
 
@@ -396,7 +396,7 @@ def run_import(args) -> None:
         restored_profiles = []
         if profiles_dir.is_dir():
             try:
-                from hermes_cli.profiles import (
+                from hermes_agent.cli.profiles import (
                     create_wrapper_script, check_alias_collision,
                     _is_wrapper_dir_in_path, _get_wrapper_dir,
                 )

hermes_agent/cli/claw.py

@@ -16,9 +16,9 @@ import sys
 from datetime import datetime
 from pathlib import Path
 
-from hermes_cli.config import get_hermes_home, get_config_path, load_config, save_config
-from hermes_constants import get_optional_skills_dir
-from hermes_cli.setup import (
+from hermes_agent.cli.config import get_hermes_home, get_config_path, load_config, save_config
+from hermes_agent.constants import get_optional_skills_dir
+from hermes_agent.cli.setup_wizard import (
     Colors,
     color,
     print_header,
@@ -30,7 +30,7 @@ from hermes_cli.setup import (
 
 logger = logging.getLogger(__name__)
 
-PROJECT_ROOT = Path(__file__).parent.parent.resolve()
+PROJECT_ROOT = Path(__file__).resolve().parents[2].resolve()
 
 _OPENCLAW_SCRIPT = (
     get_optional_skills_dir(PROJECT_ROOT / "optional-skills")
@@ -153,7 +153,7 @@ def _warn_if_gateway_running(auto_yes: bool) -> None:
     (e.g. Telegram 409 "terminated by other getUpdates request"). Warn the
     user and let them decide whether to continue.
     """
-    from gateway.status import get_running_pid, read_runtime_status
+    from hermes_agent.gateway.status import get_running_pid, read_runtime_status
 
     if not get_running_pid():
         return

hermes_agent/cli/clipboard.py

@@ -19,7 +19,7 @@ import subprocess
 import sys
 from pathlib import Path
 
-from hermes_constants import is_wsl as _is_wsl
+from hermes_agent.constants import is_wsl as _is_wsl
 
 logger = logging.getLogger(__name__)
 
@@ -276,7 +276,7 @@ def _get_ps_exe() -> str | None:
     global _ps_exe
     if _ps_exe is False:
         _ps_exe = _find_powershell()
-    return _ps_exe
+    return _ps_exe if isinstance(_ps_exe, str) else None
 
 
 def _windows_has_image() -> bool:
@@ -395,14 +395,17 @@ def _wayland_save(dest: Path) -> bool:
 
 def _convert_to_png(path: Path) -> bool:
     """Convert an image file to PNG in-place (requires Pillow or ImageMagick)."""
-    # Try Pillow first (likely installed in the venv)
     try:
         from PIL import Image
+    except ImportError:
+        raise ImportError(
+            "Pillow is required for clipboard image conversion. "
+            "Install with: pip install hermes-agent[cli]"
+        ) from None
+    try:
         img = Image.open(path)
         img.save(path, "PNG")
         return True
-    except ImportError:
-        pass
     except Exception as e:
         logger.debug("Pillow BMP→PNG conversion failed: %s", e)
 

hermes_agent/cli/commands.py

@@ -318,7 +318,7 @@ def _resolve_config_gates() -> set[str]:
     if not gated:
         return set()
     try:
-        from hermes_cli.config import read_raw_config
+        from hermes_agent.cli.config import read_raw_config
         cfg = read_raw_config()
     except Exception:
         return set()
@@ -497,7 +497,7 @@ def _collect_gateway_skill_entries(
     # --- Tier 1: Plugin slash commands (never trimmed) ---------------------
     plugin_pairs: list[tuple[str, str]] = []
     try:
-        from hermes_cli.plugins import get_plugin_commands
+        from hermes_agent.cli.plugins import get_plugin_commands
         plugin_cmds = get_plugin_commands()
         for cmd_name in sorted(plugin_cmds):
             name = sanitize_name(cmd_name) if sanitize_name else cmd_name
@@ -519,15 +519,15 @@ def _collect_gateway_skill_entries(
     # --- Tier 2: Built-in skill commands (trimmed at cap) -----------------
     _platform_disabled: set[str] = set()
     try:
-        from agent.skill_utils import get_disabled_skill_names
+        from hermes_agent.agent.skill_utils import get_disabled_skill_names
         _platform_disabled = get_disabled_skill_names(platform=platform)
     except Exception:
         pass
 
     skill_triples: list[tuple[str, str, str]] = []
     try:
-        from agent.skill_commands import get_skill_commands
-        from tools.skills_tool import SKILLS_DIR
+        from hermes_agent.agent.skill_commands import get_skill_commands
+        from hermes_agent.tools.skills.tool import SKILLS_DIR
         _skills_dir = str(SKILLS_DIR.resolve())
         _hub_dir = str((SKILLS_DIR / ".hub").resolve())
         skill_cmds = get_skill_commands()
@@ -661,7 +661,7 @@ def discord_skill_commands_by_category(
 
     _platform_disabled: set[str] = set()
     try:
-        from agent.skill_utils import get_disabled_skill_names
+        from hermes_agent.agent.skill_utils import get_disabled_skill_names
         _platform_disabled = get_disabled_skill_names(platform="discord")
     except Exception:
         pass
@@ -673,8 +673,8 @@ def discord_skill_commands_by_category(
     hidden = 0
 
     try:
-        from agent.skill_commands import get_skill_commands
-        from tools.skills_tool import SKILLS_DIR
+        from hermes_agent.agent.skill_commands import get_skill_commands
+        from hermes_agent.tools.skills.tool import SKILLS_DIR
         _skills_dir = SKILLS_DIR.resolve()
         _hub_dir = (SKILLS_DIR / ".hub").resolve()
         skill_cmds = get_skill_commands()
@@ -1116,7 +1116,7 @@ class SlashCommandCompleter(Completer):
     def _skin_completions(sub_text: str, sub_lower: str):
         """Yield completions for /skin from available skins."""
         try:
-            from hermes_cli.skin_engine import list_skins
+            from hermes_agent.cli.ui.skin_engine import list_skins
             for s in list_skins():
                 name = s["name"]
                 if name.startswith(sub_lower) and name != sub_lower:
@@ -1133,7 +1133,7 @@ class SlashCommandCompleter(Completer):
     def _personality_completions(sub_text: str, sub_lower: str):
         """Yield completions for /personality from configured personalities."""
         try:
-            from hermes_cli.config import load_config
+            from hermes_agent.cli.config import load_config
             personalities = load_config().get("agent", {}).get("personalities", {})
             if "none".startswith(sub_lower) and "none" != sub_lower:
                 yield Completion(
@@ -1162,7 +1162,7 @@ class SlashCommandCompleter(Completer):
         seen = set()
         # Config-based direct aliases (preferred — include provider info)
         try:
-            from hermes_cli.model_switch import (
+            from hermes_agent.cli.models.switch import (
                 _ensure_direct_aliases, DIRECT_ALIASES, MODEL_ALIASES,
             )
             _ensure_direct_aliases()
@@ -1262,7 +1262,7 @@ class SlashCommandCompleter(Completer):
 
         # Plugin-registered slash commands
         try:
-            from hermes_cli.plugins import get_plugin_commands
+            from hermes_agent.cli.plugins import get_plugin_commands
             for cmd_name, cmd_info in get_plugin_commands().items():
                 if cmd_name.startswith(word):
                     desc = str(cmd_info.get("description", "Plugin command"))

hermes_agent/cli/config.py

@@ -23,7 +23,7 @@ import sys
 import tempfile
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Dict, Any, Optional, List, Tuple
+from typing import Dict, Any, Optional, List, Tuple, TypedDict, Union
 
 logger = logging.getLogger(__name__)
 
@@ -61,8 +61,8 @@ _EXTRA_ENV_KEYS = frozenset({
 })
 import yaml
 
-from hermes_cli.colors import Colors, color
-from hermes_cli.default_soul import DEFAULT_SOUL_MD
+from hermes_agent.cli.ui.colors import Colors, color
+from hermes_agent.cli.default_soul import DEFAULT_SOUL_MD
 
 
 # =============================================================================
@@ -169,7 +169,7 @@ def get_container_exec_info() -> Optional[dict]:
     if os.environ.get("HERMES_DEV") == "1":
         return None
 
-    from hermes_constants import is_container
+    from hermes_agent.constants import is_container
     if is_container():
         return None
 
@@ -205,7 +205,7 @@ def get_container_exec_info() -> Optional[dict]:
 # =============================================================================
 
 # Re-export from hermes_constants — canonical definition lives there.
-from hermes_constants import get_hermes_home  # noqa: F811,E402
+from hermes_agent.constants import get_hermes_home  # noqa: F811,E402
 
 def get_config_path() -> Path:
     """Get the main config file path."""
@@ -217,7 +217,7 @@ def get_env_path() -> Path:
 
 def get_project_root() -> Path:
     """Get the project installation directory."""
-    return Path(__file__).parent.parent.resolve()
+    return Path(__file__).resolve().parents[2].resolve()
 
 def _secure_dir(path):
     """Set directory to owner-only access (0700 by default). No-op on Windows.
@@ -343,12 +343,363 @@ def _ensure_hermes_home_managed(home: Path):
 # Config loading/saving
 # =============================================================================
 
-DEFAULT_CONFIG = {
+class _AgentConfig(TypedDict):
+    max_turns: int
+    gateway_timeout: int
+    restart_drain_timeout: int
+    service_tier: str
+    tool_use_enforcement: str
+    gateway_timeout_warning: int
+    gateway_notify_interval: int
+
+class _TerminalConfig(TypedDict):
+    backend: str
+    modal_mode: str
+    cwd: str
+    timeout: int
+    env_passthrough: List[str]
+    docker_image: str
+    docker_forward_env: List[str]
+    docker_env: Dict[str, str]
+    singularity_image: str
+    modal_image: str
+    daytona_image: str
+    container_cpu: int
+    container_memory: int
+    container_disk: int
+    container_persistent: bool
+    docker_volumes: List[str]
+    docker_mount_cwd_to_workspace: bool
+    persistent_shell: bool
+
+
+class _CamofoxConfig(TypedDict, total=False):
+    managed_persistence: bool
+
+
+class _BrowserConfig(TypedDict):
+    inactivity_timeout: int
+    command_timeout: int
+    record_sessions: bool
+    allow_private_urls: bool
+    cdp_url: str
+    camofox: _CamofoxConfig
+
+
+class _CheckpointsConfig(TypedDict):
+    enabled: bool
+    max_snapshots: int
+
+
+class _CompressionConfig(TypedDict):
+    enabled: bool
+    threshold: float
+    target_ratio: float
+    protect_last_n: int
+
+
+class _BedrockDiscoveryConfig(TypedDict):
+    enabled: bool
+    provider_filter: List[str]
+    refresh_interval: int
+
+
+class _BedrockGuardrailConfig(TypedDict):
+    guardrail_identifier: str
+    guardrail_version: str
+    stream_processing_mode: str
+    trace: str
+
+
+class _BedrockConfig(TypedDict):
+    region: str
+    discovery: _BedrockDiscoveryConfig
+    guardrail: _BedrockGuardrailConfig
+
+
+class _AuxiliaryTaskConfig(TypedDict, total=False):
+    provider: str
+    model: str
+    base_url: str
+    api_key: str
+    timeout: int
+    extra_body: Dict[str, Any]
+    max_concurrency: int
+    download_timeout: int
+
+
+class _AuxiliaryConfig(TypedDict):
+    vision: _AuxiliaryTaskConfig
+    web_extract: _AuxiliaryTaskConfig
+    compression: _AuxiliaryTaskConfig
+    session_search: _AuxiliaryTaskConfig
+    skills_hub: _AuxiliaryTaskConfig
+    approval: _AuxiliaryTaskConfig
+    mcp: _AuxiliaryTaskConfig
+    flush_memories: _AuxiliaryTaskConfig
+    title_generation: _AuxiliaryTaskConfig
+
+
+class _UserMessagePreviewConfig(TypedDict):
+    first_lines: int
+    last_lines: int
+
+
+class _DisplayConfig(TypedDict):
+    compact: bool
+    personality: str
+    resume_display: str
+    busy_input_mode: str
+    bell_on_complete: bool
+    show_reasoning: bool
+    streaming: bool
+    final_response_markdown: str
+    inline_diffs: bool
+    show_cost: bool
+    skin: str
+    user_message_preview: _UserMessagePreviewConfig
+    interim_assistant_messages: bool
+    tool_progress_command: bool
+    tool_progress_overrides: Dict[str, Any]
+    tool_preview_length: int
+    platforms: Dict[str, Any]
+
+
+class _DashboardConfig(TypedDict):
+    theme: str
+
+
+class _PrivacyConfig(TypedDict):
+    redact_pii: bool
+
+
+class _EdgeTtsConfig(TypedDict):
+    voice: str
+
+
+class _ElevenlabsTtsConfig(TypedDict):
+    voice_id: str
+    model_id: str
+
+
+class _OpenaiTtsConfig(TypedDict):
+    model: str
+    voice: str
+
+
+class _XaiTtsConfig(TypedDict):
+    voice_id: str
+    language: str
+    sample_rate: int
+    bit_rate: int
+
+
+class _MistralTtsConfig(TypedDict):
+    model: str
+    voice_id: str
+
+
+class _NeuttsConfig(TypedDict):
+    ref_audio: str
+    ref_text: str
+    model: str
+    device: str
+
+
+class _TtsConfig(TypedDict):
+    provider: str
+    edge: _EdgeTtsConfig
+    elevenlabs: _ElevenlabsTtsConfig
+    openai: _OpenaiTtsConfig
+    xai: _XaiTtsConfig
+    mistral: _MistralTtsConfig
+    neutts: _NeuttsConfig
+
+
+class _LocalSttConfig(TypedDict):
+    model: str
+    language: str
+
+
+class _OpenaiSttConfig(TypedDict):
+    model: str
+
+
+class _MistralSttConfig(TypedDict):
+    model: str
+
+
+class _SttConfig(TypedDict):
+    enabled: bool
+    provider: str
+    local: _LocalSttConfig
+    openai: _OpenaiSttConfig
+    mistral: _MistralSttConfig
+
+
+class _VoiceConfig(TypedDict):
+    record_key: str
+    max_recording_seconds: int
+    auto_tts: bool
+    silence_threshold: int
+    silence_duration: float
+
+
+class _HumanDelayConfig(TypedDict):
+    mode: str
+    min_ms: int
+    max_ms: int
+
+
+class _ContextConfig(TypedDict):
+    engine: str
+
+
+class _MemoryConfig(TypedDict):
+    memory_enabled: bool
+    user_profile_enabled: bool
+    memory_char_limit: int
+    user_char_limit: int
+    provider: str
+
+
+class _DelegationConfig(TypedDict):
+    model: str
+    provider: str
+    base_url: str
+    api_key: str
+    max_iterations: int
+    reasoning_effort: str
+
+
+class _SkillsConfig(TypedDict):
+    external_dirs: List[str]
+
+
+class _ChannelPromptsConfig(TypedDict):
+    channel_prompts: Dict[str, str]
+
+
+class _DiscordConfig(TypedDict):
+    require_mention: bool
+    free_response_channels: str
+    allowed_channels: str
+    auto_thread: bool
+    reactions: bool
+    channel_prompts: Dict[str, str]
+    server_actions: str
+
+
+class _ApprovalsConfig(TypedDict):
+    mode: str
+    timeout: int
+    cron_mode: str
+
+
+class _WebsiteBlocklistConfig(TypedDict):
+    enabled: bool
+    domains: List[str]
+    shared_files: List[str]
+
+
+class _SecurityConfig(TypedDict):
+    redact_secrets: bool
+    tirith_enabled: bool
+    tirith_path: str
+    tirith_timeout: int
+    tirith_fail_open: bool
+    website_blocklist: _WebsiteBlocklistConfig
+
+
+class _CronConfig(TypedDict):
+    wrap_response: bool
+    max_parallel_jobs: Optional[int]
+
+
+class _CodeExecutionConfig(TypedDict):
+    mode: str
+
+
+class _LoggingConfig(TypedDict):
+    level: str
+    max_size_mb: int
+    backup_count: int
+
+
+class _NetworkConfig(TypedDict):
+    force_ipv4: bool
+
+
+class _DefaultConfig(TypedDict):
+    model: str
+    providers: Dict[str, Any]
+    fallback_providers: List[Any]
+    credential_pool_strategies: Dict[str, Any]
+    toolsets: List[str]
+    agent: _AgentConfig
+    terminal: _TerminalConfig
+    browser: _BrowserConfig
+    checkpoints: _CheckpointsConfig
+    file_read_max_chars: int
+    compression: _CompressionConfig
+    bedrock: _BedrockConfig
+    auxiliary: _AuxiliaryConfig
+    display: _DisplayConfig
+    dashboard: _DashboardConfig
+    privacy: _PrivacyConfig
+    tts: _TtsConfig
+    stt: _SttConfig
+    voice: _VoiceConfig
+    human_delay: _HumanDelayConfig
+    context: _ContextConfig
+    memory: _MemoryConfig
+    delegation: _DelegationConfig
+    prefill_messages_file: str
+    skills: _SkillsConfig
+    honcho: Dict[str, Any]
+    timezone: str
+    discord: _DiscordConfig
+    whatsapp: Dict[str, Any]
+    telegram: _ChannelPromptsConfig
+    slack: _ChannelPromptsConfig
+    mattermost: _ChannelPromptsConfig
+    approvals: _ApprovalsConfig
+    command_allowlist: List[str]
+    quick_commands: Dict[str, Any]
+    hooks: Dict[str, Any]
+    hooks_auto_accept: bool
+    personalities: Dict[str, Any]
+    security: _SecurityConfig
+    cron: _CronConfig
+    code_execution: _CodeExecutionConfig
+    logging: _LoggingConfig
+    network: _NetworkConfig
+    _config_version: int
+
+
+class _EnvVarRequired(TypedDict):
+    description: str
+    prompt: str
+    category: str
+
+
+class _EnvVarOptional(TypedDict, total=False):
+    url: Optional[str]
+    password: bool
+    tools: List[str]
+    advanced: bool
+
+
+class _EnvVarInfo(_EnvVarRequired, _EnvVarOptional):
+    pass
+
+
+DEFAULT_CONFIG: _DefaultConfig = {
     "model": "",
     "providers": {},
     "fallback_providers": [],
     "credential_pool_strategies": {},
-    "toolsets": ["hermes-cli"],
+    "hermes_agent.tools.toolsets": ["hermes-cli"],
     "agent": {
         "max_turns": 90,
         # Inactivity timeout for gateway agent execution (seconds).
@@ -919,7 +1270,7 @@ ENV_VARS_BY_VERSION: Dict[int, List[str]] = {
 REQUIRED_ENV_VARS = {}
 
 # Optional environment variables that enhance functionality
-OPTIONAL_ENV_VARS = {
+OPTIONAL_ENV_VARS: Dict[str, _EnvVarInfo] = {
     # ── Provider (handled in provider selection, not shown in checklists) ──
     "NOUS_BASE_URL": {
         "description": "Nous Portal base URL override",
@@ -1853,7 +2204,7 @@ def get_missing_config_fields() -> List[Dict[str, Any]]:
     config = load_config()
     missing = []
 
-    def _check(defaults: dict, current: dict, prefix: str = ""):
+    def _check(defaults: Dict[str, Any], current: Dict[str, Any], prefix: str = ""):
         for key, default_value in defaults.items():
             if key.startswith('_'):
                 continue
@@ -1867,7 +2218,7 @@ def get_missing_config_fields() -> List[Dict[str, Any]]:
             elif isinstance(default_value, dict) and isinstance(current.get(key), dict):
                 _check(default_value, current[key], full_key)
 
-    _check(DEFAULT_CONFIG, config)
+    _check(dict(DEFAULT_CONFIG), config)
     return missing
 
 
@@ -1879,7 +2230,7 @@ def get_missing_skill_config_vars() -> List[Dict[str, Any]]:
     config.yaml.  Returns a list of dicts suitable for prompting.
     """
     try:
-        from agent.skill_utils import discover_all_skill_config_vars, SKILL_CONFIG_PREFIX
+        from hermes_agent.agent.skill_utils import discover_all_skill_config_vars, SKILL_CONFIG_PREFIX
     except Exception:
         return []
 
@@ -2087,8 +2438,8 @@ def check_config_version() -> Tuple[int, int]:
     Returns (current_version, latest_version).
     """
     config = load_config()
-    current = config.get("_config_version", 0)
-    latest = DEFAULT_CONFIG.get("_config_version", 1)
+    current = int(config.get("_config_version", 0))
+    latest = int(DEFAULT_CONFIG.get("_config_version", 1))
     return current, latest
 
 
@@ -2099,7 +2450,7 @@ def check_config_version() -> Tuple[int, int]:
 # Fields that are valid at root level of config.yaml
 _KNOWN_ROOT_KEYS = {
     "_config_version", "model", "providers", "fallback_model",
-    "fallback_providers", "credential_pool_strategies", "toolsets",
+    "fallback_providers", "credential_pool_strategies", "hermes_agent.tools.toolsets",
     "agent", "terminal", "display", "compression", "delegation",
     "auxiliary", "custom_providers", "context", "memory", "gateway",
 }
@@ -2781,7 +3132,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
             print()
             config = load_config()
             try:
-                from agent.skill_utils import SKILL_CONFIG_PREFIX
+                from hermes_agent.agent.skill_utils import SKILL_CONFIG_PREFIX
             except Exception:
                 SKILL_CONFIG_PREFIX = "skills.config"
             for var in missing_skill_config:
@@ -2807,7 +3158,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
     return results
 
 
-def _deep_merge(base: dict, override: dict) -> dict:
+def _deep_merge(base: Dict[str, Any], override: Dict[str, Any]) -> Dict[str, Any]:
     """Recursively merge *override* into *base*, preserving nested defaults.
 
     Keys in *override* take precedence. If both values are dicts the merge
@@ -2996,7 +3347,7 @@ def load_config() -> Dict[str, Any]:
     ensure_hermes_home()
     config_path = get_config_path()
     
-    config = copy.deepcopy(DEFAULT_CONFIG)
+    config: Dict[str, Any] = copy.deepcopy(DEFAULT_CONFIG)
     
     if config_path.exists():
         try:
@@ -3096,7 +3447,7 @@ def save_config(config: Dict[str, Any]):
     if is_managed():
         managed_error("save configuration")
         return
-    from utils import atomic_yaml_write
+    from hermes_agent.utils import atomic_yaml_write
 
     ensure_hermes_home()
     config_path = get_config_path()
@@ -3532,7 +3883,7 @@ def show_config():
     for env_key, name in keys:
         value = get_env_value(env_key)
         print(f"  {name:<14} {redact_key(value)}")
-    from hermes_cli.auth import get_anthropic_key
+    from hermes_agent.cli.auth.auth import get_anthropic_key
     anthropic_value = get_anthropic_key()
     print(f"  {'Anthropic':<14} {redact_key(anthropic_value)}")
     
@@ -3640,7 +3991,7 @@ def show_config():
     
     # Skill config
     try:
-        from agent.skill_utils import discover_all_skill_config_vars, resolve_skill_config_values
+        from hermes_agent.agent.skill_utils import discover_all_skill_config_vars, resolve_skill_config_values
         skill_vars = discover_all_skill_config_vars()
         if skill_vars:
             resolved = resolve_skill_config_values(skill_vars)
@@ -3672,7 +4023,7 @@ def edit_config():
     
     # Ensure config exists
     if not config_path.exists():
-        save_config(DEFAULT_CONFIG)
+        save_config(dict(DEFAULT_CONFIG))
         print(f"Created {config_path}")
     
     # Find editor
@@ -3754,7 +4105,7 @@ def set_config_value(key: str, value: str):
     
     # Write only user config back (not the full merged defaults)
     ensure_hermes_home()
-    from utils import atomic_yaml_write
+    from hermes_agent.utils import atomic_yaml_write
     atomic_yaml_write(config_path, user_config, sort_keys=False)
     
     # Keep .env in sync for keys that terminal_tool reads directly from env vars.

hermes_agent/cli/cron.py

@@ -10,10 +10,9 @@ import sys
 from pathlib import Path
 from typing import Iterable, List, Optional
 
-PROJECT_ROOT = Path(__file__).parent.parent.resolve()
-sys.path.insert(0, str(PROJECT_ROOT))
+PROJECT_ROOT = Path(__file__).resolve().parents[2].resolve()
 
-from hermes_cli.colors import Colors, color
+from hermes_agent.cli.ui.colors import Colors, color
 
 
 def _normalize_skills(single_skill=None, skills: Optional[Iterable[str]] = None) -> Optional[List[str]]:
@@ -33,14 +32,14 @@ def _normalize_skills(single_skill=None, skills: Optional[Iterable[str]] = None)
 
 
 def _cron_api(**kwargs):
-    from tools.cronjob_tools import cronjob as cronjob_tool
+    from hermes_agent.tools.cronjob import cronjob as cronjob_tool
 
     return json.loads(cronjob_tool(**kwargs))
 
 
 def cron_list(show_all: bool = False):
     """List all scheduled jobs."""
-    from cron.jobs import list_jobs
+    from hermes_agent.cron.jobs import list_jobs
 
     jobs = list_jobs(include_disabled=show_all)
 
@@ -110,7 +109,7 @@ def cron_list(show_all: bool = False):
 
         print()
 
-    from hermes_cli.gateway import find_gateway_pids
+    from hermes_agent.cli.gateway import find_gateway_pids
     if not find_gateway_pids():
         print(color("  ⚠  Gateway is not running — jobs won't fire automatically.", Colors.YELLOW))
         print(color("     Start it with: hermes gateway install", Colors.DIM))
@@ -120,14 +119,14 @@ def cron_list(show_all: bool = False):
 
 def cron_tick():
     """Run due jobs once and exit."""
-    from cron.scheduler import tick
+    from hermes_agent.cron.scheduler import tick
     tick(verbose=True)
 
 
 def cron_status():
     """Show cron execution status."""
-    from cron.jobs import list_jobs
-    from hermes_cli.gateway import find_gateway_pids
+    from hermes_agent.cron.jobs import list_jobs
+    from hermes_agent.cli.gateway import find_gateway_pids
 
     print()
 
@@ -185,7 +184,7 @@ def cron_create(args):
 
 
 def cron_edit(args):
-    from cron.jobs import get_job
+    from hermes_agent.cron.jobs import get_job
 
     job = get_job(args.job_id)
     if not job:

hermes_agent/cli/debug.py

@@ -16,7 +16,7 @@ import urllib.request
 from pathlib import Path
 from typing import Optional
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 
 # ---------------------------------------------------------------------------
@@ -319,7 +319,7 @@ def _resolve_log_path(log_name: str) -> Optional[Path]:
 
     Returns the path if found, or None.
     """
-    from hermes_cli.logs import LOG_FILES
+    from hermes_agent.cli.logs import LOG_FILES
 
     filename = LOG_FILES.get(log_name)
     if not filename:
@@ -340,7 +340,7 @@ def _resolve_log_path(log_name: str) -> Optional[Path]:
 
 def _read_log_tail(log_name: str, num_lines: int) -> str:
     """Read the last *num_lines* from a log file, or return a placeholder."""
-    from hermes_cli.logs import _read_last_n_lines
+    from hermes_agent.cli.logs import _read_last_n_lines
 
     log_path = _resolve_log_path(log_name)
     if log_path is None:
@@ -388,7 +388,7 @@ def _read_full_log(log_name: str, max_bytes: int = _MAX_LOG_BYTES) -> Optional[s
 
 def _capture_dump() -> str:
     """Run ``hermes dump`` and return its stdout as a string."""
-    from hermes_cli.dump import run_dump
+    from hermes_agent.cli.dump import run_dump
 
     class _FakeArgs:
         show_keys = False

hermes_agent/cli/doctor.py

@@ -10,8 +10,8 @@ import subprocess
 import shutil
 from pathlib import Path
 
-from hermes_cli.config import get_project_root, get_hermes_home, get_env_path
-from hermes_constants import display_hermes_home
+from hermes_agent.cli.config import get_project_root, get_hermes_home, get_env_path
+from hermes_agent.constants import display_hermes_home
 
 PROJECT_ROOT = get_project_root()
 HERMES_HOME = get_hermes_home()
@@ -28,9 +28,9 @@ if _env_path.exists():
 # Also try project .env as dev fallback
 load_dotenv(PROJECT_ROOT / ".env", override=False, encoding="utf-8")
 
-from hermes_cli.colors import Colors, color
-from hermes_constants import OPENROUTER_MODELS_URL
-from utils import base_url_host_matches
+from hermes_agent.cli.ui.colors import Colors, color
+from hermes_agent.constants import OPENROUTER_MODELS_URL
+from hermes_agent.utils import base_url_host_matches
 
 
 _PROVIDER_ENV_HINTS = (
@@ -58,7 +58,7 @@ _PROVIDER_ENV_HINTS = (
 )
 
 
-from hermes_constants import is_termux as _is_termux
+from hermes_agent.constants import is_termux as _is_termux
 
 
 def _python_install_cmd() -> str:
@@ -92,7 +92,7 @@ def _has_provider_env_config(content: str) -> bool:
 def _honcho_is_configured_for_doctor() -> bool:
     """Return True when Honcho is configured, even if this process has no active session."""
     try:
-        from plugins.memory.honcho.client import HonchoClientConfig
+        from hermes_agent.plugins.memory.honcho.client import HonchoClientConfig
 
         cfg = HonchoClientConfig.from_global_config()
         return bool(cfg.enabled and (cfg.api_key or cfg.base_url))
@@ -132,7 +132,7 @@ def check_info(text: str):
 def _check_gateway_service_linger(issues: list[str]) -> None:
     """Warn when a systemd user gateway service will stop after logout."""
     try:
-        from hermes_cli.gateway import (
+        from hermes_agent.cli.gateway import (
             get_systemd_linger_status,
             get_systemd_unit_path,
             is_linux,
@@ -290,12 +290,12 @@ def run_doctor(args):
 
             known_providers: set = set()
             try:
-                from hermes_cli.auth import PROVIDER_REGISTRY
+                from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
                 known_providers = set(PROVIDER_REGISTRY.keys()) | {"openrouter", "custom", "auto"}
             except Exception:
                 pass
             try:
-                from hermes_cli.auth import resolve_provider as _resolve_provider
+                from hermes_agent.cli.auth.auth import resolve_provider as _resolve_provider
             except Exception:
                 _resolve_provider = None
 
@@ -338,7 +338,7 @@ def run_doctor(args):
             # explicitly dispatch, which would produce false positives.
             if canonical_provider and canonical_provider not in ("auto", "custom", "openrouter"):
                 try:
-                    from hermes_cli.auth import PROVIDER_REGISTRY, get_auth_status
+                    from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY, get_auth_status
                     pconfig = PROVIDER_REGISTRY.get(canonical_provider)
                     if pconfig and getattr(pconfig, "auth_type", "") == "api_key":
                         status = get_auth_status(canonical_provider) or {}
@@ -379,7 +379,7 @@ def run_doctor(args):
     config_path = HERMES_HOME / 'config.yaml'
     if config_path.exists():
         try:
-            from hermes_cli.config import check_config_version, migrate_config
+            from hermes_agent.cli.config import check_config_version, migrate_config
             current_ver, latest_ver = check_config_version()
             if current_ver < latest_ver:
                 check_warn(
@@ -419,7 +419,7 @@ def run_doctor(args):
                             model_section[k] = raw_config.pop(k)
                         else:
                             raw_config.pop(k)
-                    from utils import atomic_yaml_write
+                    from hermes_agent.utils import atomic_yaml_write
                     atomic_yaml_write(config_path, raw_config)
                     check_ok("Migrated stale root-level keys into model section")
                     fixed_count += 1
@@ -430,7 +430,7 @@ def run_doctor(args):
 
         # Validate config structure (catches malformed custom_providers, etc.)
         try:
-            from hermes_cli.config import validate_config_structure
+            from hermes_agent.cli.config import validate_config_structure
             config_issues = validate_config_structure()
             if config_issues:
                 print()
@@ -454,7 +454,7 @@ def run_doctor(args):
     print(color("◆ Auth Providers", Colors.CYAN, Colors.BOLD))
 
     try:
-        from hermes_cli.auth import (
+        from hermes_agent.cli.auth.auth import (
             get_nous_auth_status,
             get_codex_auth_status,
             get_gemini_oauth_auth_status,
@@ -877,13 +877,13 @@ def run_doctor(args):
     else:
         check_warn("OpenRouter API", "(not configured)")
     
-    from hermes_cli.auth import get_anthropic_key
+    from hermes_agent.cli.auth.auth import get_anthropic_key
     anthropic_key = get_anthropic_key()
     if anthropic_key:
         print("  Checking Anthropic API...", end="", flush=True)
         try:
             import httpx
-            from agent.anthropic_adapter import _is_oauth_token, _COMMON_BETAS, _OAUTH_ONLY_BETAS
+            from hermes_agent.providers.anthropic_adapter import _is_oauth_token, _COMMON_BETAS, _OAUTH_ONLY_BETAS
 
             headers = {"anthropic-version": "2023-06-01"}
             if _is_oauth_token(anthropic_key):
@@ -951,7 +951,7 @@ def run_doctor(args):
                 # with no /v1) don't support /models.  Rewrite to the OpenAI-compat
                 # /v1 surface for health checks.
                 if _base and _base.rstrip("/").endswith("/anthropic"):
-                    from agent.auxiliary_client import _to_openai_base_url
+                    from hermes_agent.providers.auxiliary import _to_openai_base_url
                     _base = _to_openai_base_url(_base)
                 if base_url_host_matches(_base, "api.kimi.com") and _base.rstrip("/").endswith("/coding"):
                     _base = _base.rstrip("/") + "/v1"
@@ -977,7 +977,7 @@ def run_doctor(args):
     # -- AWS Bedrock --
     # Bedrock uses the AWS SDK credential chain, not API keys.
     try:
-        from agent.bedrock_adapter import has_aws_credentials, resolve_aws_auth_env_var, resolve_bedrock_region
+        from hermes_agent.providers.bedrock_adapter import has_aws_credentials, resolve_aws_auth_env_var, resolve_bedrock_region
         if has_aws_credentials():
             _auth_var = resolve_aws_auth_env_var()
             _region = resolve_bedrock_region()
@@ -1028,9 +1028,7 @@ def run_doctor(args):
     print(color("◆ Tool Availability", Colors.CYAN, Colors.BOLD))
     
     try:
-        # Add project root to path for imports
-        sys.path.insert(0, str(PROJECT_ROOT))
-        from model_tools import check_tool_availability, TOOLSET_REQUIREMENTS
+        from hermes_agent.tools.dispatch import check_tool_availability, TOOLSET_REQUIREMENTS
         
         available, unavailable = check_tool_availability()
         available, unavailable = _apply_doctor_tool_availability_overrides(available, unavailable)
@@ -1079,7 +1077,7 @@ def run_doctor(args):
     else:
         check_warn("Skills Hub directory not initialized", "(run: hermes skills list)")
 
-    from hermes_cli.config import get_env_value
+    from hermes_agent.cli.config import get_env_value
     github_token = get_env_value("GITHUB_TOKEN") or get_env_value("GH_TOKEN")
     if github_token:
         check_ok("GitHub token configured (authenticated API access)")
@@ -1107,7 +1105,7 @@ def run_doctor(args):
         check_ok("Built-in memory active", "(no external provider configured — this is fine)")
     elif _active_memory_provider == "honcho":
         try:
-            from plugins.memory.honcho.client import HonchoClientConfig, resolve_config_path
+            from hermes_agent.plugins.memory.honcho.client import HonchoClientConfig, resolve_config_path
             hcfg = HonchoClientConfig.from_global_config()
             _honcho_cfg_path = resolve_config_path()
 
@@ -1119,7 +1117,7 @@ def run_doctor(args):
                 check_fail("Honcho API key or base URL not set", "run: hermes memory setup")
                 issues.append("No Honcho API key — run 'hermes memory setup'")
             else:
-                from plugins.memory.honcho.client import get_honcho_client, reset_honcho_client
+                from hermes_agent.plugins.memory.honcho.client import get_honcho_client, reset_honcho_client
                 reset_honcho_client()
                 try:
                     get_honcho_client(hcfg)
@@ -1137,7 +1135,7 @@ def run_doctor(args):
             check_warn("Honcho check failed", str(_e))
     elif _active_memory_provider == "mem0":
         try:
-            from plugins.memory.mem0 import _load_config as _load_mem0_config
+            from hermes_agent.plugins.memory.mem0 import _load_config as _load_mem0_config
             mem0_cfg = _load_mem0_config()
             mem0_key = mem0_cfg.get("api_key", "")
             if mem0_key:
@@ -1154,7 +1152,7 @@ def run_doctor(args):
     else:
         # Generic check for other memory providers (openviking, hindsight, etc.)
         try:
-            from plugins.memory import load_memory_provider
+            from hermes_agent.plugins.memory import load_memory_provider
             _provider = load_memory_provider(_active_memory_provider)
             if _provider and _provider.is_available():
                 check_ok(f"{_active_memory_provider} provider active")
@@ -1169,7 +1167,7 @@ def run_doctor(args):
     # Profiles
     # =========================================================================
     try:
-        from hermes_cli.profiles import list_profiles, _get_wrapper_dir, profile_exists
+        from hermes_agent.cli.profiles import list_profiles, _get_wrapper_dir, profile_exists
         import re as _re
 
         named_profiles = [p for p in list_profiles() if not p.is_default]

hermes_agent/cli/dump.py

@@ -13,8 +13,8 @@ import subprocess
 import sys
 from pathlib import Path
 
-from hermes_cli.config import get_hermes_home, get_env_path, get_project_root, load_config
-from hermes_constants import display_hermes_home
+from hermes_agent.cli.config import get_hermes_home, get_env_path, get_project_root, load_config
+from hermes_agent.constants import display_hermes_home
 
 
 def _get_git_commit(project_root: Path) -> str:
@@ -44,7 +44,7 @@ def _redact(value: str) -> str:
 def _gateway_status() -> str:
     """Return a short gateway status string."""
     try:
-        from hermes_cli.gateway import get_gateway_runtime_snapshot
+        from hermes_agent.cli.gateway import get_gateway_runtime_snapshot
 
         snapshot = get_gateway_runtime_snapshot()
         if snapshot.running:
@@ -142,7 +142,7 @@ def _config_overrides(config: dict) -> dict[str, str]:
     
     Returns a flat dict of dotpath -> value for interesting overrides.
     """
-    from hermes_cli.config import DEFAULT_CONFIG
+    from hermes_agent.cli.config import DEFAULT_CONFIG
 
     overrides = {}
 
@@ -178,7 +178,7 @@ def _config_overrides(config: dict) -> dict[str, str]:
     default_toolsets = DEFAULT_CONFIG.get("toolsets", [])
     user_toolsets = config.get("toolsets", [])
     if user_toolsets != default_toolsets:
-        overrides["toolsets"] = str(user_toolsets)
+        overrides["hermes_agent.tools.toolsets"] = str(user_toolsets)
 
     # Fallback providers
     fallbacks = config.get("fallback_providers", [])
@@ -207,7 +207,7 @@ def run_dump(args):
     hermes_home = get_hermes_home()
 
     try:
-        from hermes_cli import __version__, __release_date__
+        from hermes_agent.cli import __version__, __release_date__
     except ImportError:
         __version__ = "(unknown)"
         __release_date__ = ""
@@ -223,7 +223,7 @@ def run_dump(args):
 
     # Profile
     try:
-        from hermes_cli.profiles import get_active_profile_name
+        from hermes_agent.cli.profiles import get_active_profile_name
         profile = get_active_profile_name() or "(default)"
     except Exception:
         profile = "(default)"

hermes_agent/cli/env_loader.py

@@ -108,7 +108,7 @@ def _sanitize_env_file_if_needed(path: Path) -> None:
     if not path.exists():
         return
     try:
-        from hermes_cli.config import _sanitize_env_lines
+        from hermes_agent.cli.config import _sanitize_env_lines
     except ImportError:
         return  # early bootstrap — config module not available yet
 

hermes_agent/cli/gateway.py

@@ -13,15 +13,15 @@ import sys
 from dataclasses import dataclass
 from pathlib import Path
 
-PROJECT_ROOT = Path(__file__).parent.parent.resolve()
+PROJECT_ROOT = Path(__file__).resolve().parents[2].resolve()
 
-from gateway.status import terminate_pid
-from gateway.restart import (
+from hermes_agent.gateway.status import terminate_pid
+from hermes_agent.gateway.restart import (
     DEFAULT_GATEWAY_RESTART_DRAIN_TIMEOUT,
     GATEWAY_SERVICE_RESTART_EXIT_CODE,
     parse_restart_drain_timeout,
 )
-from hermes_cli.config import (
+from hermes_agent.cli.config import (
     get_env_value,
     get_hermes_home,
     is_managed,
@@ -31,11 +31,11 @@ from hermes_cli.config import (
 )
 # display_hermes_home is imported lazily at call sites to avoid ImportError
 # when hermes_constants is cached from a pre-update version during `hermes update`.
-from hermes_cli.setup import (
+from hermes_agent.cli.setup_wizard import (
     print_header, print_info, print_success, print_warning, print_error,
     prompt, prompt_choice, prompt_yes_no,
 )
-from hermes_cli.colors import Colors, color
+from hermes_agent.cli.ui.colors import Colors, color
 
 
 # =============================================================================
@@ -192,6 +192,12 @@ def _scan_gateway_pids(exclude_pids: set[int], all_profiles: bool = False) -> li
     """
     pids: list[int] = []
     patterns = [
+        "hermes_agent.cli.main gateway",
+        "hermes_agent.cli.main --profile",
+        "hermes_agent.cli.main -p",
+        "hermes_agent/cli/main.py gateway",
+        "hermes_agent/cli/main.py --profile",
+        "hermes_agent/cli/main.py -p",
         "hermes_cli.main gateway",
         "hermes_cli.main --profile",
         "hermes_cli.main -p",
@@ -303,7 +309,7 @@ def find_gateway_pids(exclude_pids: set | None = None, all_profiles: bool = Fals
     pids: list[int] = []
     if not all_profiles:
         try:
-            from gateway.status import get_running_pid
+            from hermes_agent.gateway.status import get_running_pid
 
             _append_unique_pid(pids, get_running_pid(), _exclude)
         except Exception:
@@ -357,7 +363,7 @@ def get_gateway_runtime_snapshot(system: bool = False) -> GatewayRuntimeSnapshot
             gateway_pids=gateway_pids,
         )
 
-    from hermes_constants import is_container
+    from hermes_agent.constants import is_container
 
     if is_linux() and is_container():
         return GatewayRuntimeSnapshot(
@@ -445,7 +451,7 @@ def stop_profile_gateway() -> bool:
     Returns True if a process was stopped, False if none was found.
     """
     try:
-        from gateway.status import get_running_pid, remove_pid_file
+        from hermes_agent.gateway.status import get_running_pid, remove_pid_file
     except ImportError:
         return False
 
@@ -478,7 +484,7 @@ def is_linux() -> bool:
     return sys.platform.startswith('linux')
 
 
-from hermes_constants import is_container, is_termux, is_wsl
+from hermes_agent.constants import is_container, is_termux, is_wsl
 
 
 def _wsl_systemd_operational() -> bool:
@@ -552,7 +558,7 @@ def _profile_suffix() -> str:
     """
     import hashlib
     import re
-    from hermes_constants import get_default_hermes_root
+    from hermes_agent.constants import get_default_hermes_root
     home = get_hermes_home().resolve()
     default = get_default_hermes_root().resolve()
     if home == default:
@@ -582,7 +588,7 @@ def _profile_arg(hermes_home: str | None = None) -> str:
             service definition for a different user (e.g. system service).
     """
     import re
-    from hermes_constants import get_default_hermes_root
+    from hermes_agent.constants import get_default_hermes_root
     home = Path(hermes_home or str(get_hermes_home())).resolve()
     default = get_default_hermes_root().resolve()
     if home == default:
@@ -696,6 +702,8 @@ _LEGACY_SERVICE_NAMES: tuple[str, ...] = ("hermes.service",)
 # ExecStart content markers that identify a unit as running our gateway.
 # A legacy unit is only flagged when its file contains one of these.
 _LEGACY_UNIT_EXECSTART_MARKERS: tuple[str, ...] = (
+    "hermes_agent.cli.main gateway",
+    "hermes_agent/cli/main.py gateway",
     "hermes_cli.main gateway",
     "hermes_cli/main.py gateway",
     "gateway/run.py",
@@ -1221,7 +1229,7 @@ StartLimitBurst=5
 Type=simple
 User={username}
 Group={group_name}
-ExecStart={python_path} -m hermes_cli.main{f" {profile_arg}" if profile_arg else ""} gateway run --replace
+ExecStart={python_path} -m hermes_agent.cli.main{f" {profile_arg}" if profile_arg else ""} gateway run --replace
 WorkingDirectory={working_dir}
 Environment="HOME={home_dir}"
 Environment="USER={username}"
@@ -1256,7 +1264,7 @@ StartLimitBurst=5
 
 [Service]
 Type=simple
-ExecStart={python_path} -m hermes_cli.main{f" {profile_arg}" if profile_arg else ""} gateway run --replace
+ExecStart={python_path} -m hermes_agent.cli.main{f" {profile_arg}" if profile_arg else ""} gateway run --replace
 WorkingDirectory={working_dir}
 Environment="PATH={sane_path}"
 Environment="VIRTUAL_ENV={venv_dir}"
@@ -1501,7 +1509,7 @@ def systemd_restart(system: bool = False):
     if system:
         _require_root_for_system_service("restart")
     refresh_systemd_unit_if_needed(system=system)
-    from gateway.status import get_running_pid
+    from hermes_agent.gateway.status import get_running_pid
 
     pid = get_running_pid()
     if pid is not None and _request_gateway_self_restart(pid):
@@ -1689,7 +1697,7 @@ def generate_launchd_plist() -> str:
     prog_args = [
         f"<string>{python_path}</string>",
         "<string>-m</string>",
-        "<string>hermes_cli.main</string>",
+        "<string>hermes_agent.cli.main</string>",
     ]
     if profile_arg:
         for part in profile_arg.split():
@@ -1799,7 +1807,7 @@ def launchd_install(force: bool = False):
     print()
     print("Next steps:")
     print("  hermes gateway status             # Check status")
-    from hermes_constants import display_hermes_home as _dhh
+    from hermes_agent.constants import display_hermes_home as _dhh
     print(f"  tail -f {_dhh()}/logs/gateway.log  # View logs")
 
 def launchd_uninstall():
@@ -1867,7 +1875,7 @@ def _wait_for_gateway_exit(timeout: float = 10.0, force_after: float | None = 5.
         force_after: Seconds of graceful waiting before escalating to force-kill.
     """
     import time
-    from gateway.status import get_running_pid
+    from hermes_agent.gateway.status import get_running_pid
 
     deadline = time.monotonic() + timeout
     force_deadline = (time.monotonic() + force_after) if force_after is not None else None
@@ -1901,7 +1909,7 @@ def launchd_restart():
     label = get_launchd_label()
     target = f"{_launchd_domain()}/{label}"
     drain_timeout = _get_restart_drain_timeout()
-    from gateway.status import get_running_pid
+    from hermes_agent.gateway.status import get_running_pid
 
     try:
         pid = get_running_pid()
@@ -1982,9 +1990,7 @@ def run_gateway(verbose: int = 0, quiet: bool = False, replace: bool = False):
                  This prevents systemd restart loops when the old process
                  hasn't fully exited yet.
     """
-    sys.path.insert(0, str(PROJECT_ROOT))
-    
-    from gateway.run import start_gateway
+    from hermes_agent.gateway.run import start_gateway
     
     print("┌─────────────────────────────────────────────────────────┐")
     print("│           ⚕ Hermes Gateway Starting...                 │")
@@ -2430,7 +2436,7 @@ def _platform_status(platform: dict) -> str:
 def _runtime_health_lines() -> list[str]:
     """Summarize the latest persisted gateway runtime health state."""
     try:
-        from gateway.status import read_runtime_status
+        from hermes_agent.gateway.status import read_runtime_status
     except Exception:
         return []
 
@@ -2562,7 +2568,7 @@ def _setup_standard_platform(platform: dict):
 
 def _setup_whatsapp():
     """Delegate to the existing WhatsApp setup flow."""
-    from hermes_cli.main import cmd_whatsapp
+    from hermes_agent.cli.main import cmd_whatsapp
     import argparse
     cmd_whatsapp(argparse.Namespace())
 
@@ -2581,7 +2587,7 @@ def _setup_sms():
 
 def _setup_dingtalk():
     """Configure DingTalk — QR scan (recommended) or manual credential entry."""
-    from hermes_cli.setup import (
+    from hermes_agent.cli.setup_wizard import (
         prompt_choice, prompt_yes_no, print_info, print_success, print_warning,
     )
 
@@ -2612,7 +2618,7 @@ def _setup_dingtalk():
     if method == 0:
         # ── QR-code device-flow authorization ──
         try:
-            from hermes_cli.dingtalk_auth import dingtalk_qr_auth
+            from hermes_agent.cli.auth.dingtalk import dingtalk_qr_auth
         except ImportError as exc:
             print_warning(f"  QR auth module failed to load ({exc}), falling back to manual input.")
             _setup_standard_platform(dingtalk_platform)
@@ -2644,6 +2650,12 @@ def _setup_wecom():
     _setup_standard_platform(wecom_platform)
 
 
+def _setup_wecom_callback():
+    """Configure WeCom Callback (self-built app) via the standard platform setup."""
+    wecom_platform = next(p for p in _PLATFORMS if p["key"] == "wecom_callback")
+    _setup_standard_platform(wecom_platform)
+
+
 def _is_service_installed() -> bool:
     """Check if the gateway is installed as a system service."""
     if supports_systemd_services():
@@ -2714,7 +2726,7 @@ def _setup_weixin():
             return
 
     try:
-        from gateway.platforms.weixin import check_weixin_requirements, qr_login
+        from hermes_agent.gateway.platforms.weixin import check_weixin_requirements, qr_login
     except Exception as exc:
         print_error(f"  Weixin adapter import failed: {exc}")
         print_info("  Install gateway dependencies first, then retry.")
@@ -2849,7 +2861,7 @@ def _setup_feishu():
     if method_idx == 0:
         # ── QR scan-to-create ──
         try:
-            from gateway.platforms.feishu import qr_register
+            from hermes_agent.gateway.platforms.feishu import qr_register
         except Exception as exc:
             print_error(f"  Feishu / Lark onboard import failed: {exc}")
             qr_register = None
@@ -2890,7 +2902,7 @@ def _setup_feishu():
         # Try to probe the bot with manual credentials
         bot_name = None
         try:
-            from gateway.platforms.feishu import probe_bot
+            from hermes_agent.gateway.platforms.feishu import probe_bot
             bot_info = probe_bot(app_id, app_secret, domain)
             if bot_info:
                 bot_name = bot_info.get("bot_name")
@@ -3123,11 +3135,11 @@ def _qqbot_qr_flow():
     or None on failure/cancel.
     """
     try:
-        from gateway.platforms.qqbot import (
+        from hermes_agent.gateway.platforms.qqbot import (
             create_bind_task, poll_bind_result, build_connect_url,
             decrypt_secret, BindStatus,
         )
-        from gateway.platforms.qqbot.constants import ONBOARD_POLL_INTERVAL
+        from hermes_agent.gateway.platforms.qqbot.constants import ONBOARD_POLL_INTERVAL
     except Exception as exc:
         print_error(f"  QQBot onboard import failed: {exc}")
         return None
@@ -3465,7 +3477,7 @@ def gateway_setup():
                 print_info("  To enable systemd: add systemd=true to /etc/wsl.conf, then 'wsl --shutdown'")
             else:
                 if is_termux():
-                    from hermes_constants import display_hermes_home as _dhh
+                    from hermes_agent.constants import display_hermes_home as _dhh
                     print_info("  Termux does not use systemd/launchd services.")
                     print_info("  Run in foreground: hermes gateway run")
                     print_info(f"  Or start it manually in the background (best effort): nohup hermes gateway run >{_dhh()}/logs/gateway.log 2>&1 &")

hermes_agent/cli/hooks.py

@@ -50,8 +50,8 @@ def hooks_command(args) -> None:
 # ---------------------------------------------------------------------------
 
 def _cmd_list(_args) -> None:
-    from hermes_cli.config import load_config
-    from agent import shell_hooks
+    from hermes_agent.cli.config import load_config
+    from hermes_agent.agent import shell_hooks
 
     specs = shell_hooks.iter_configured_hooks(load_config())
 
@@ -186,9 +186,9 @@ _DEFAULT_PAYLOADS = {
 
 
 def _cmd_test(args) -> None:
-    from hermes_cli.config import load_config
-    from hermes_cli.plugins import VALID_HOOKS
-    from agent import shell_hooks
+    from hermes_agent.cli.config import load_config
+    from hermes_agent.cli.plugins import VALID_HOOKS
+    from hermes_agent.agent import shell_hooks
 
     event = args.event
     if event not in VALID_HOOKS:
@@ -273,7 +273,7 @@ def _truncate(s: str, n: int) -> str:
 # ---------------------------------------------------------------------------
 
 def _cmd_revoke(args) -> None:
-    from agent import shell_hooks
+    from hermes_agent.agent import shell_hooks
 
     removed = shell_hooks.revoke(args.command)
     if removed == 0:
@@ -291,8 +291,8 @@ def _cmd_revoke(args) -> None:
 # ---------------------------------------------------------------------------
 
 def _cmd_doctor(_args) -> None:
-    from hermes_cli.config import load_config
-    from agent import shell_hooks
+    from hermes_agent.cli.config import load_config
+    from hermes_agent.agent import shell_hooks
 
     specs = shell_hooks.iter_configured_hooks(load_config())
 

hermes_agent/cli/logs.py

@@ -24,7 +24,7 @@ from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Optional, Sequence
 
-from hermes_constants import get_hermes_home, display_hermes_home
+from hermes_agent.constants import get_hermes_home, display_hermes_home
 
 # Known log files (name → filename)
 LOG_FILES = {
@@ -191,7 +191,7 @@ def tail_log(
     # Resolve component to logger name prefixes
     component_prefixes = None
     if component:
-        from hermes_logging import COMPONENT_PREFIXES
+        from hermes_agent.logging import COMPONENT_PREFIXES
         component_lower = component.lower()
         if component_lower not in COMPONENT_PREFIXES:
             available = ", ".join(sorted(COMPONENT_PREFIXES))

hermes_agent/cli/mcp_config.py

@@ -15,15 +15,15 @@ import re
 import time
 from typing import Any, Dict, List, Optional, Tuple
 
-from hermes_cli.config import (
+from hermes_agent.cli.config import (
     load_config,
     save_config,
     get_env_value,
     save_env_value,
     get_hermes_home,  # noqa: F401 — used by test mocks
 )
-from hermes_cli.colors import Colors, color
-from hermes_constants import display_hermes_home
+from hermes_agent.cli.ui.colors import Colors, color
+from hermes_agent.constants import display_hermes_home
 
 logger = logging.getLogger(__name__)
 
@@ -61,7 +61,7 @@ def _confirm(question: str, default: bool = True) -> bool:
 
 
 def _prompt(question: str, *, password: bool = False, default: str = "") -> str:
-    from hermes_cli.cli_output import prompt as _shared_prompt
+    from hermes_agent.cli.ui.output import prompt as _shared_prompt
     return _shared_prompt(question, default=default, password=password)
 
 
@@ -165,7 +165,7 @@ def _probe_single_server(
     Returns list of ``(tool_name, description)`` tuples.
     Raises on connection failure.
     """
-    from tools.mcp_tool import (
+    from hermes_agent.tools.mcp.tool import (
         _ensure_mcp_loop,
         _run_on_mcp_loop,
         _connect_server,
@@ -279,7 +279,7 @@ def cmd_mcp_add(args):
         _info(f"Starting OAuth flow for '{name}'...")
         oauth_ok = False
         try:
-            from tools.mcp_oauth_manager import get_manager
+            from hermes_agent.tools.mcp.oauth_manager import get_manager
             oauth_auth = get_manager().get_or_build_provider(name, url, None)
             if oauth_auth:
                 server_config["auth"] = "oauth"
@@ -372,7 +372,7 @@ def cmd_mcp_add(args):
 
     if choice in ("s", "select"):
         # Interactive tool selection
-        from hermes_cli.curses_ui import curses_checklist
+        from hermes_agent.cli.ui.curses import curses_checklist
 
         labels = [f"{t[0]}  —  {t[1]}" for t in tools]
         pre_selected = set(range(len(tools)))
@@ -432,7 +432,7 @@ def cmd_mcp_remove(args):
     # any provider instance cached in the current process (e.g. from an
     # earlier `hermes mcp test` in the same session) is evicted too.
     try:
-        from tools.mcp_oauth_manager import get_manager
+        from hermes_agent.tools.mcp.oauth_manager import get_manager
         get_manager().remove(name)
         _success("Cleaned up OAuth tokens")
     except Exception:
@@ -616,7 +616,7 @@ def cmd_mcp_login(args):
     # Wipe both disk and in-memory cache so the next probe forces a fresh
     # OAuth flow.
     try:
-        from tools.mcp_oauth_manager import get_manager
+        from hermes_agent.tools.mcp.oauth_manager import get_manager
         mgr = get_manager()
         mgr.remove(name)
     except Exception as exc:
@@ -700,7 +700,7 @@ def cmd_mcp_configure(args):
     print()
 
     # Interactive checklist
-    from hermes_cli.curses_ui import curses_checklist
+    from hermes_agent.cli.ui.curses import curses_checklist
 
     labels = [f"{t[0]}  —  {t[1]}" for t in all_tools]
 
@@ -742,7 +742,7 @@ def mcp_command(args):
     action = getattr(args, "mcp_action", None)
 
     if action == "serve":
-        from mcp_serve import run_mcp_server
+        from hermes_agent.tools.mcp.serve import run_mcp_server
         run_mcp_server(verbose=getattr(args, "verbose", False))
         return
 

hermes_agent/cli/memory_setup.py

@@ -12,7 +12,7 @@ import os
 import sys
 from pathlib import Path
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 
 # ---------------------------------------------------------------------------
@@ -25,7 +25,7 @@ def _curses_select(title: str, items: list[tuple[str, str]], default: int = 0) -
     items: list of (label, description) tuples.
     Returns selected index, or default on escape/quit.
     """
-    from hermes_cli.curses_ui import curses_radiolist
+    from hermes_agent.cli.ui.curses import curses_radiolist
     # Format (label, desc) tuples into display strings
     display_items = [
         f"{label}  {desc}" if desc else label
@@ -58,7 +58,7 @@ def _prompt(label: str, default: str | None = None, secret: bool = False) -> str
 def _install_dependencies(provider_name: str) -> None:
     """Install pip dependencies declared in plugin.yaml."""
     import subprocess
-    from plugins.memory import find_provider_dir
+    from hermes_agent.plugins.memory import find_provider_dir
 
     plugin_dir = find_provider_dir(provider_name)
     if not plugin_dir:
@@ -148,7 +148,7 @@ def _get_available_providers() -> list:
     Returns list of (name, description, provider_instance) tuples.
     """
     try:
-        from plugins.memory import discover_memory_providers, load_memory_provider
+        from hermes_agent.plugins.memory import discover_memory_providers, load_memory_provider
         raw = discover_memory_providers()
     except Exception:
         raw = []
@@ -184,7 +184,7 @@ def _get_available_providers() -> list:
 
 def cmd_setup_provider(provider_name: str) -> None:
     """Run memory setup for a specific provider, skipping the picker."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
 
     providers = _get_available_providers()
     match = None
@@ -220,7 +220,7 @@ def cmd_setup_provider(provider_name: str) -> None:
 
 def cmd_setup(args) -> None:
     """Interactive memory provider setup wizard."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
 
     providers = _get_available_providers()
 
@@ -386,7 +386,7 @@ def _write_env_vars(env_path: Path, env_writes: dict) -> None:
 
 def cmd_status(args) -> None:
     """Show current memory provider config."""
-    from hermes_cli.config import load_config
+    from hermes_agent.cli.config import load_config
 
     config = load_config()
     mem_config = config.get("memory", {})

hermes_agent/cli/models/models.py

@@ -16,7 +16,7 @@ from difflib import get_close_matches
 from pathlib import Path
 from typing import Any, NamedTuple, Optional
 
-from hermes_cli import __version__ as _HERMES_VERSION
+from hermes_agent.cli import __version__ as _HERMES_VERSION
 
 # Identify ourselves so endpoints fronted by Cloudflare's Browser Integrity
 # Check (error 1010) don't reject the default ``Python-urllib/*`` signature.
@@ -101,7 +101,7 @@ def _codex_curated_models() -> list[str]:
     This keeps the gateway /model picker in sync with the CLI `hermes model`
     flow without maintaining a separate static list.
     """
-    from hermes_cli.codex_models import DEFAULT_CODEX_MODELS, _add_forward_compat_models
+    from hermes_agent.cli.models.codex import DEFAULT_CODEX_MODELS, _add_forward_compat_models
     return _add_forward_compat_models(list(DEFAULT_CODEX_MODELS))
 
 
@@ -488,7 +488,7 @@ def check_nous_free_tier() -> bool:
             return cached_result
 
     try:
-        from hermes_cli.auth import get_provider_auth_state, resolve_nous_runtime_credentials
+        from hermes_agent.cli.auth.auth import get_provider_auth_state, resolve_nous_runtime_credentials
 
         # Ensure we have a fresh token (triggers refresh if needed)
         resolve_nous_runtime_credentials(min_key_ttl_seconds=60)
@@ -583,7 +583,7 @@ def fetch_nous_recommended_models(
 def _resolve_nous_portal_url() -> str:
     """Best-effort lookup of the Portal base URL the user is authed against."""
     try:
-        from hermes_cli.auth import (
+        from hermes_agent.cli.auth.auth import (
             DEFAULT_NOUS_PORTAL_URL,
             get_provider_auth_state,
         )
@@ -912,7 +912,7 @@ def fetch_ai_gateway_models(
     if _ai_gateway_catalog_cache is not None and not force_refresh:
         return list(_ai_gateway_catalog_cache)
 
-    from hermes_constants import AI_GATEWAY_BASE_URL
+    from hermes_agent.constants import AI_GATEWAY_BASE_URL
 
     fallback = list(VERCEL_AI_GATEWAY_MODELS)
     preferred_ids = [mid for mid, _ in fallback]
@@ -1133,7 +1133,7 @@ def fetch_ai_gateway_pricing(
     ``prompt`` / ``completion``. This translates. Cache read/write field names
     already match.
     """
-    from hermes_constants import AI_GATEWAY_BASE_URL
+    from hermes_agent.constants import AI_GATEWAY_BASE_URL
 
     cache_key = AI_GATEWAY_BASE_URL.rstrip("/")
     if not force_refresh and cache_key in _pricing_cache:
@@ -1180,7 +1180,7 @@ def _resolve_openrouter_api_key() -> str:
 def _resolve_nous_pricing_credentials() -> tuple[str, str]:
     """Return ``(api_key, base_url)`` for Nous Portal pricing, or empty strings."""
     try:
-        from hermes_cli.auth import resolve_nous_runtime_credentials
+        from hermes_agent.cli.auth.auth import resolve_nous_runtime_credentials
         creds = resolve_nous_runtime_credentials()
         if creds:
             return (creds.get("api_key", ""), creds.get("base_url", ""))
@@ -1248,7 +1248,7 @@ def list_available_providers() -> list[dict[str, str]]:
         # Check if this provider has credentials available
         has_creds = False
         try:
-            from hermes_cli.auth import get_auth_status, has_usable_secret
+            from hermes_agent.cli.auth.auth import get_auth_status, has_usable_secret
             if pid == "custom":
                 custom_base_url = _get_custom_base_url() or ""
                 has_creds = bool(custom_base_url.strip())
@@ -1307,7 +1307,7 @@ def parse_model_input(raw: str, current_provider: str) -> tuple[str, str]:
 def _get_custom_base_url() -> str:
     """Get the custom endpoint base_url from config.yaml."""
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         model_cfg = config.get("model", {})
         if isinstance(model_cfg, dict):
@@ -1401,7 +1401,7 @@ def detect_provider_for_model(
         # credential pool, or auth store entries.
         has_creds = False
         try:
-            from hermes_cli.auth import PROVIDER_REGISTRY
+            from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
             pconfig = PROVIDER_REGISTRY.get(direct_match)
             if pconfig:
                 for env_var in pconfig.api_key_env_vars:
@@ -1414,7 +1414,7 @@ def detect_provider_for_model(
         # Claude Code tokens, and other non-env-var credentials (#10300).
         if not has_creds:
             try:
-                from agent.credential_pool import load_pool
+                from hermes_agent.providers.credential_pool import load_pool
                 pool = load_pool(direct_match)
                 if pool.has_credentials():
                     has_creds = True
@@ -1422,7 +1422,7 @@ def detect_provider_for_model(
                 pass
         if not has_creds:
             try:
-                from hermes_cli.auth import _load_auth_store
+                from hermes_agent.cli.auth.auth import _load_auth_store
                 store = _load_auth_store()
                 if direct_match in store.get("providers", {}) or direct_match in store.get("credential_pool", {}):
                     has_creds = True
@@ -1572,7 +1572,7 @@ def resolve_fast_mode_overrides(model_id: Optional[str]) -> dict[str, Any] | Non
 def _resolve_copilot_catalog_api_key() -> str:
     """Best-effort GitHub token for fetching the Copilot model catalog."""
     try:
-        from hermes_cli.auth import resolve_api_key_provider_credentials
+        from hermes_agent.cli.auth.auth import resolve_api_key_provider_credentials
 
         creds = resolve_api_key_provider_credentials("copilot")
         return str(creds.get("api_key") or "").strip()
@@ -1590,7 +1590,7 @@ def provider_model_ids(provider: Optional[str], *, force_refresh: bool = False)
     if normalized == "openrouter":
         return model_ids(force_refresh=force_refresh)
     if normalized == "openai-codex":
-        from hermes_cli.codex_models import get_codex_model_ids
+        from hermes_agent.cli.models.codex import get_codex_model_ids
 
         return get_codex_model_ids()
     if normalized in {"copilot", "copilot-acp"}:
@@ -1605,7 +1605,7 @@ def provider_model_ids(provider: Optional[str], *, force_refresh: bool = False)
     if normalized == "nous":
         # Try live Nous Portal /models endpoint
         try:
-            from hermes_cli.auth import fetch_nous_models, resolve_nous_runtime_credentials
+            from hermes_agent.cli.auth.auth import fetch_nous_models, resolve_nous_runtime_credentials
             creds = resolve_nous_runtime_credentials()
             if creds:
                 live = fetch_nous_models(api_key=creds.get("api_key", ""), inference_base_url=creds.get("base_url", ""))
@@ -1647,7 +1647,7 @@ def _fetch_anthropic_models(timeout: float = 5.0) -> Optional[list[str]]:
     Claude Code auto-discovery).  Returns sorted model IDs or None.
     """
     try:
-        from agent.anthropic_adapter import resolve_anthropic_token, _is_oauth_token
+        from hermes_agent.providers.anthropic_adapter import resolve_anthropic_token, _is_oauth_token
     except ImportError:
         return None
 
@@ -1658,7 +1658,7 @@ def _fetch_anthropic_models(timeout: float = 5.0) -> Optional[list[str]]:
     headers: dict[str, str] = {"anthropic-version": "2023-06-01"}
     if _is_oauth_token(token):
         headers["Authorization"] = f"Bearer {token}"
-        from agent.anthropic_adapter import _COMMON_BETAS, _OAUTH_ONLY_BETAS
+        from hermes_agent.providers.anthropic_adapter import _COMMON_BETAS, _OAUTH_ONLY_BETAS
         headers["anthropic-beta"] = ",".join(_COMMON_BETAS + _OAUTH_ONLY_BETAS)
     else:
         headers["x-api-key"] = token
@@ -1701,7 +1701,7 @@ def copilot_default_headers() -> dict[str, str]:
     Copilot CLI send on every request.
     """
     try:
-        from hermes_cli.copilot_auth import copilot_request_headers
+        from hermes_agent.cli.auth.copilot import copilot_request_headers
         return copilot_request_headers(is_agent_turn=True)
     except ImportError:
         return {
@@ -2117,7 +2117,7 @@ def _fetch_ai_gateway_models(timeout: float = 5.0) -> Optional[list[str]]:
         return None
     base_url = os.getenv("AI_GATEWAY_BASE_URL", "").strip()
     if not base_url:
-        from hermes_constants import AI_GATEWAY_BASE_URL
+        from hermes_agent.constants import AI_GATEWAY_BASE_URL
         base_url = AI_GATEWAY_BASE_URL
 
     url = base_url.rstrip("/") + "/models"
@@ -2161,7 +2161,7 @@ _OLLAMA_CLOUD_CACHE_TTL = 3600  # 1 hour
 
 def _ollama_cloud_cache_path() -> Path:
     """Return the path for the Ollama Cloud model cache."""
-    from hermes_constants import get_hermes_home
+    from hermes_agent.constants import get_hermes_home
     return get_hermes_home() / "ollama_cloud_models_cache.json"
 
 
@@ -2195,7 +2195,7 @@ def _load_ollama_cloud_cache(*, ignore_ttl: bool = False) -> Optional[dict]:
 def _save_ollama_cloud_cache(models: list[str]) -> None:
     """Persist the merged Ollama Cloud model list to disk."""
     try:
-        from utils import atomic_json_write
+        from hermes_agent.utils import atomic_json_write
         cache_path = _ollama_cloud_cache_path()
         cache_path.parent.mkdir(parents=True, exist_ok=True)
         atomic_json_write(cache_path, {"models": models, "cached_at": time.time()}, indent=None)
@@ -2240,7 +2240,7 @@ def fetch_ollama_cloud_models(
     # 3. models.dev registry
     mdev_models: list[str] = []
     try:
-        from agent.models_dev import list_agentic_models
+        from hermes_agent.providers.metadata_dev import list_agentic_models
         mdev_models = list_agentic_models("ollama-cloud")
     except Exception:
         pass
@@ -2510,7 +2510,7 @@ def validate_requested_model(
     # AWS SDK control plane (ListFoundationModels + ListInferenceProfiles).
     if normalized == "bedrock":
         try:
-            from agent.bedrock_adapter import discover_bedrock_models, resolve_bedrock_region
+            from hermes_agent.providers.bedrock_adapter import discover_bedrock_models, resolve_bedrock_region
             region = resolve_bedrock_region()
             discovered = discover_bedrock_models(region)
             discovered_ids = {m["id"] for m in discovered}

hermes_agent/cli/models/normalize.py

@@ -184,7 +184,7 @@ def _normalize_provider_alias(provider_name: str) -> str:
     if not raw:
         return raw
     try:
-        from hermes_cli.models import normalize_provider
+        from hermes_agent.cli.models.models import normalize_provider
 
         return normalize_provider(raw)
     except Exception:
@@ -382,7 +382,7 @@ def normalize_model_for_provider(model_input: str, target_provider: str) -> str:
     #     HTTP 400 "model_not_supported".  See issue #6879.
     if provider in {"copilot", "copilot-acp"}:
         try:
-            from hermes_cli.models import normalize_copilot_model_id
+            from hermes_agent.cli.models.models import normalize_copilot_model_id
 
             normalized = normalize_copilot_model_id(name)
             if normalized:

hermes_agent/cli/models/switch.py

@@ -25,17 +25,17 @@ import re
 from dataclasses import dataclass
 from typing import List, NamedTuple, Optional
 
-from hermes_cli.providers import (
+from hermes_agent.cli.providers import (
     custom_provider_slug,
     determine_api_mode,
     get_label,
     is_aggregator,
     resolve_provider_full,
 )
-from hermes_cli.model_normalize import (
+from hermes_agent.cli.models.normalize import (
     normalize_model_for_provider,
 )
-from agent.models_dev import (
+from hermes_agent.providers.metadata_dev import (
     ModelCapabilities,
     ModelInfo,
     get_model_capabilities,
@@ -193,7 +193,7 @@ def _load_direct_aliases() -> dict[str, DirectAlias]:
     """
     merged = dict(_BUILTIN_DIRECT_ALIASES)
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         cfg = load_config()
         user_aliases = cfg.get("model_aliases")
         if isinstance(user_aliases, dict):
@@ -456,13 +456,13 @@ def switch_model(
     Returns:
         ModelSwitchResult with all information the caller needs.
     """
-    from hermes_cli.models import (
+    from hermes_agent.cli.models.models import (
         copilot_model_api_mode,
         detect_provider_for_model,
         validate_requested_model,
         opencode_model_api_mode,
     )
-    from hermes_cli.runtime_provider import resolve_runtime_provider
+    from hermes_agent.cli.runtime_provider import resolve_runtime_provider
 
     resolved_alias = ""
     new_model = raw_input.strip()
@@ -486,7 +486,7 @@ def switch_model(
             )
             # Check for common config issues that cause provider resolution failures
             try:
-                from hermes_cli.config import validate_config_structure
+                from hermes_agent.cli.config import validate_config_structure
                 _cfg_issues = validate_config_structure()
                 if _cfg_issues:
                     _switch_err += "\n\nRun 'hermes doctor' — config issues detected:"
@@ -505,7 +505,7 @@ def switch_model(
         # If no model specified, try auto-detect from endpoint
         if not new_model:
             if pdef.base_url:
-                from hermes_cli.runtime_provider import _auto_detect_local_model
+                from hermes_agent.cli.runtime_provider import _auto_detect_local_model
                 detected = _auto_detect_local_model(pdef.base_url)
                 if detected:
                     new_model = detected
@@ -804,13 +804,13 @@ def list_authenticated_providers(
     Only includes providers that have API keys set or are user-defined endpoints.
     """
     import os
-    from agent.models_dev import (
+    from hermes_agent.providers.metadata_dev import (
         PROVIDER_TO_MODELS_DEV,
         fetch_models_dev,
         get_provider_info as _mdev_pinfo,
     )
-    from hermes_cli.auth import PROVIDER_REGISTRY
-    from hermes_cli.models import OPENROUTER_MODELS, _PROVIDER_MODELS
+    from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
+    from hermes_agent.cli.models.models import OPENROUTER_MODELS, _PROVIDER_MODELS
 
     results: List[dict] = []
     seen_slugs: set = set()  # lowercase-normalized to catch case variants (#9545)
@@ -826,7 +826,7 @@ def list_authenticated_providers(
         curated["nous"] = curated["openrouter"]
     # Ollama Cloud uses dynamic discovery (no static curated list)
     if "ollama-cloud" not in curated:
-        from hermes_cli.models import fetch_ollama_cloud_models
+        from hermes_agent.cli.models.models import fetch_ollama_cloud_models
         curated["ollama-cloud"] = fetch_ollama_cloud_models()
 
     # --- 1. Check Hermes-mapped providers ---
@@ -878,8 +878,8 @@ def list_authenticated_providers(
         seen_mdev_ids.add(mdev_id)
 
     # --- 2. Check Hermes-only providers (nous, openai-codex, copilot, opencode-go) ---
-    from hermes_cli.providers import HERMES_OVERLAYS
-    from hermes_cli.auth import PROVIDER_REGISTRY as _auth_registry
+    from hermes_agent.cli.providers import HERMES_OVERLAYS
+    from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY as _auth_registry
 
     # Build reverse mapping: models.dev ID → Hermes provider ID.
     # HERMES_OVERLAYS keys may be models.dev IDs (e.g. "github-copilot")
@@ -913,7 +913,7 @@ def list_authenticated_providers(
         # OAuth via external credential files).
         if not has_creds:
             try:
-                from hermes_cli.auth import _load_auth_store
+                from hermes_agent.cli.auth.auth import _load_auth_store
                 store = _load_auth_store()
                 providers_store = store.get("providers", {})
                 pool_store = store.get("credential_pool", {})
@@ -930,7 +930,7 @@ def list_authenticated_providers(
         # imports on demand but aren't in the raw auth.json yet.
         if not has_creds:
             try:
-                from agent.credential_pool import load_pool
+                from hermes_agent.providers.credential_pool import load_pool
                 pool = load_pool(hermes_slug)
                 if pool.has_credentials():
                     has_creds = True
@@ -945,7 +945,7 @@ def list_authenticated_providers(
         # configured.
         if not has_creds and hermes_slug == "anthropic":
             try:
-                from agent.anthropic_adapter import (
+                from hermes_agent.providers.anthropic_adapter import (
                     read_claude_code_credentials,
                     read_hermes_oauth_credentials,
                 )
@@ -981,7 +981,7 @@ def list_authenticated_providers(
     # in PROVIDER_TO_MODELS_DEV or HERMES_OVERLAYS (keeps /model in sync
     # with `hermes model`).
     try:
-        from hermes_cli.models import CANONICAL_PROVIDERS as _canon_provs
+        from hermes_agent.cli.models.models import CANONICAL_PROVIDERS as _canon_provs
     except ImportError:
         _canon_provs = []
 
@@ -997,7 +997,7 @@ def list_authenticated_providers(
         # Also check auth store and credential pool
         if not _cp_has_creds:
             try:
-                from hermes_cli.auth import _load_auth_store
+                from hermes_agent.cli.auth.auth import _load_auth_store
                 _cp_store = _load_auth_store()
                 _cp_providers_store = _cp_store.get("providers", {})
                 _cp_pool_store = _cp_store.get("credential_pool", {})
@@ -1010,7 +1010,7 @@ def list_authenticated_providers(
                 pass
         if not _cp_has_creds:
             try:
-                from agent.credential_pool import load_pool
+                from hermes_agent.providers.credential_pool import load_pool
                 _cp_pool = load_pool(_cp.slug)
                 if _cp_pool.has_credentials():
                     _cp_has_creds = True

hermes_agent/cli/nous_subscription.py

@@ -6,10 +6,10 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Dict, Iterable, Optional, Set
 
-from hermes_cli.auth import get_nous_auth_status
-from hermes_cli.config import get_env_value, load_config
-from tools.managed_tool_gateway import is_managed_tool_gateway_ready
-from tools.tool_backend_helpers import (
+from hermes_agent.cli.auth.auth import get_nous_auth_status
+from hermes_agent.cli.config import get_env_value, load_config
+from hermes_agent.tools.managed_gateway import is_managed_tool_gateway_ready
+from hermes_agent.tools.backend_helpers import (
     fal_key_is_configured,
     has_direct_modal_credentials,
     managed_nous_tools_enabled,
@@ -82,7 +82,7 @@ def _model_config_dict(config: Dict[str, object]) -> Dict[str, object]:
 
 
 def _toolset_enabled(config: Dict[str, object], toolset_key: str) -> bool:
-    from toolsets import resolve_toolset
+    from hermes_agent.tools.toolsets import resolve_toolset
 
     platform_toolsets = config.get("platform_toolsets")
     if not isinstance(platform_toolsets, dict) or not platform_toolsets:
@@ -123,7 +123,7 @@ def _has_agent_browser() -> bool:
 
     agent_browser_bin = shutil.which("agent-browser")
     local_bin = (
-        Path(__file__).parent.parent / "node_modules" / ".bin" / "agent-browser"
+        Path(__file__).resolve().parents[2] / "node_modules" / ".bin" / "agent-browser"
     )
     return bool(agent_browser_bin or local_bin.exists())
 
@@ -688,7 +688,7 @@ def prompt_enable_tool_gateway(config: Dict[str, object]) -> set[str]:
         return set()
 
     try:
-        from hermes_cli.setup import prompt_choice
+        from hermes_agent.cli.setup_wizard import prompt_choice
     except Exception:
         return set()
 
@@ -766,7 +766,7 @@ def prompt_enable_tool_gateway(config: Dict[str, object]) -> set[str]:
 
     changed = apply_gateway_defaults(config, to_apply)
     if changed:
-        from hermes_cli.config import save_config
+        from hermes_agent.cli.config import save_config
         save_config(config)
         # Only report the tools that actually switched (not already-managed ones)
         newly_switched = changed - set(already_managed)

hermes_agent/cli/pairing.py

@@ -10,7 +10,7 @@ Usage:
 
 def pairing_command(args):
     """Handle hermes pairing subcommands."""
-    from gateway.pairing import PairingStore
+    from hermes_agent.gateway.pairing import PairingStore
 
     store = PairingStore()
     action = getattr(args, "pairing_action", None)

hermes_agent/cli/plugins.py

@@ -43,8 +43,8 @@ from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Set, Union
 
-from hermes_constants import get_hermes_home
-from utils import env_var_enabled
+from hermes_agent.constants import get_hermes_home
+from hermes_agent.utils import env_var_enabled
 
 try:
     import yaml
@@ -73,7 +73,7 @@ VALID_HOOKS: Set[str] = {
     "subagent_stop",
 }
 
-ENTRY_POINTS_GROUP = "hermes_agent.plugins"
+ENTRY_POINTS_GROUP = "plugins"
 
 _NS_PARENT = "hermes_plugins"
 
@@ -91,7 +91,7 @@ def _get_disabled_plugins() -> set:
     ``plugins.enabled``.
     """
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         disabled = config.get("plugins", {}).get("disabled", [])
         return set(disabled) if isinstance(disabled, list) else set()
@@ -114,7 +114,7 @@ def _get_enabled_plugins() -> Optional[set]:
     * ``set(...)`` — the concrete allow-list.
     """
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         plugins_cfg = config.get("plugins")
         if not isinstance(plugins_cfg, dict):
@@ -207,7 +207,7 @@ class PluginContext:
         emoji: str = "",
     ) -> None:
         """Register a tool in the global registry **and** track it as plugin-provided."""
-        from tools.registry import registry
+        from hermes_agent.tools.registry import registry
 
         registry.register(
             name=name,
@@ -305,7 +305,7 @@ class PluginContext:
 
         # Reject if it conflicts with a built-in command
         try:
-            from hermes_cli.commands import resolve_command
+            from hermes_agent.cli.commands import resolve_command
             if resolve_command(clean) is not None:
                 logger.warning(
                     "Plugin '%s' tried to register command '/%s' which conflicts "
@@ -341,7 +341,7 @@ class PluginContext:
         Returns:
             JSON string from the tool handler (same format as model tool calls).
         """
-        from tools.registry import registry
+        from hermes_agent.tools.registry import registry
 
         # Wire up parent agent context when available (CLI mode).
         # In gateway mode _cli_ref is None — tools degrade gracefully
@@ -372,7 +372,7 @@ class PluginContext:
             )
             return
         # Defer the import to avoid circular deps at module level
-        from agent.context_engine import ContextEngine
+        from hermes_agent.agent.context.engine import ContextEngine
         if not isinstance(engine, ContextEngine):
             logger.warning(
                 "Plugin '%s' tried to register a context engine that does not "
@@ -397,8 +397,8 @@ class PluginContext:
         ``config.yaml`` matches against when routing ``image_generate``
         tool calls.
         """
-        from agent.image_gen_provider import ImageGenProvider
-        from agent.image_gen_registry import register_provider
+        from hermes_agent.agent.image_gen.provider import ImageGenProvider
+        from hermes_agent.agent.image_gen.registry import register_provider
 
         if not isinstance(provider, ImageGenProvider):
             logger.warning(
@@ -452,7 +452,7 @@ class PluginContext:
             ValueError: if *name* contains ``':'`` or invalid characters.
             FileNotFoundError: if *path* does not exist.
         """
-        from agent.skill_utils import _NAMESPACE_RE
+        from hermes_agent.agent.skill_utils import _NAMESPACE_RE
 
         if ":" in name:
             raise ValueError(
@@ -1087,7 +1087,7 @@ def get_plugin_toolsets() -> List[tuple]:
         return []
 
     try:
-        from tools.registry import registry
+        from hermes_agent.tools.registry import registry
     except Exception:
         return []
 

hermes_agent/cli/plugins_cmd.py

@@ -17,7 +17,7 @@ import sys
 from pathlib import Path
 from typing import Optional
 
-from hermes_constants import get_hermes_home
+from hermes_agent.constants import get_hermes_home
 
 logger = logging.getLogger(__name__)
 
@@ -173,8 +173,8 @@ def _prompt_plugin_env_vars(manifest: dict, console) -> None:
     if not requires_env:
         return
 
-    from hermes_cli.config import get_env_value, save_env_value  # noqa: F811
-    from hermes_constants import display_hermes_home
+    from hermes_agent.cli.config import get_env_value, save_env_value  # noqa: F811
+    from hermes_agent.constants import display_hermes_home
 
     # Normalise to list-of-dicts
     env_specs: list[dict] = []
@@ -360,7 +360,7 @@ def cmd_install(
                 )
                 sys.exit(1)
             if mv_int > _SUPPORTED_MANIFEST_VERSION:
-                from hermes_cli.config import recommended_update_command
+                from hermes_agent.cli.config import recommended_update_command
                 console.print(
                     f"[red]Error:[/red] Plugin '{plugin_name}' requires manifest_version "
                     f"{mv}, but this installer only supports up to {_SUPPORTED_MANIFEST_VERSION}.\n"
@@ -517,7 +517,7 @@ def _get_disabled_set() -> set:
     listed in ``plugins.enabled``.
     """
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         disabled = config.get("plugins", {}).get("disabled", [])
         return set(disabled) if isinstance(disabled, list) else set()
@@ -527,7 +527,7 @@ def _get_disabled_set() -> set:
 
 def _save_disabled_set(disabled: set) -> None:
     """Write the disabled plugins list to config.yaml."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
     config = load_config()
     if "plugins" not in config:
         config["plugins"] = {}
@@ -542,7 +542,7 @@ def _get_enabled_set() -> set:
     the key is missing (same behaviour as "nothing enabled yet").
     """
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         plugins_cfg = config.get("plugins", {})
         if not isinstance(plugins_cfg, dict):
@@ -555,7 +555,7 @@ def _get_enabled_set() -> set:
 
 def _save_enabled_set(enabled: set) -> None:
     """Write the enabled plugins list to config.yaml."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
     config = load_config()
     if "plugins" not in config:
         config["plugins"] = {}
@@ -631,8 +631,8 @@ def _plugin_exists(name: str) -> bool:
                 return True
     # Bundled: <repo>/plugins/<name>/
     from pathlib import Path as _P
-    import hermes_cli
-    repo_plugins = _P(hermes_cli.__file__).resolve().parent.parent / "plugins"
+    import hermes_agent.cli as _cli_pkg
+    repo_plugins = _P(_cli_pkg.__file__).resolve().parent.parent / "plugins"
     if repo_plugins.is_dir():
         candidate = repo_plugins / name
         if candidate.is_dir() and (
@@ -659,8 +659,8 @@ def _discover_all_plugins() -> list:
     seen: dict = {}  # name -> (name, version, description, source, path)
 
     # Bundled (<repo>/plugins/<name>/), excluding memory/ and context_engine/
-    import hermes_cli
-    repo_plugins = Path(hermes_cli.__file__).resolve().parent.parent / "plugins"
+    import hermes_agent.cli as _cli_pkg
+    repo_plugins = Path(_cli_pkg.__file__).resolve().parent.parent / "plugins"
     for base, source in ((repo_plugins, "bundled"), (_plugins_dir(), "user")):
         if not base.is_dir():
             continue
@@ -743,7 +743,7 @@ def cmd_list() -> None:
 def _discover_memory_providers() -> list[tuple[str, str]]:
     """Return [(name, description), ...] for available memory providers."""
     try:
-        from plugins.memory import discover_memory_providers
+        from hermes_agent.plugins.memory import discover_memory_providers
         return [(name, desc) for name, desc, _avail in discover_memory_providers()]
     except Exception:
         return []
@@ -752,7 +752,7 @@ def _discover_memory_providers() -> list[tuple[str, str]]:
 def _discover_context_engines() -> list[tuple[str, str]]:
     """Return [(name, description), ...] for available context engines."""
     try:
-        from plugins.context_engine import discover_context_engines
+        from hermes_agent.plugins.context_engine import discover_context_engines
         return [(name, desc) for name, desc, _avail in discover_context_engines()]
     except Exception:
         return []
@@ -761,7 +761,7 @@ def _discover_context_engines() -> list[tuple[str, str]]:
 def _get_current_memory_provider() -> str:
     """Return the current memory.provider from config (empty = built-in)."""
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         return config.get("memory", {}).get("provider", "") or ""
     except Exception:
@@ -771,7 +771,7 @@ def _get_current_memory_provider() -> str:
 def _get_current_context_engine() -> str:
     """Return the current context.engine from config."""
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
         config = load_config()
         return config.get("context", {}).get("engine", "compressor") or "compressor"
     except Exception:
@@ -780,7 +780,7 @@ def _get_current_context_engine() -> str:
 
 def _save_memory_provider(name: str) -> None:
     """Persist memory.provider to config.yaml."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
     config = load_config()
     if "memory" not in config:
         config["memory"] = {}
@@ -790,7 +790,7 @@ def _save_memory_provider(name: str) -> None:
 
 def _save_context_engine(name: str) -> None:
     """Persist context.engine to config.yaml."""
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
     config = load_config()
     if "context" not in config:
         config["context"] = {}
@@ -800,7 +800,7 @@ def _save_context_engine(name: str) -> None:
 
 def _configure_memory_provider() -> bool:
     """Launch a radio picker for memory providers. Returns True if changed."""
-    from hermes_cli.curses_ui import curses_radiolist
+    from hermes_agent.cli.ui.curses import curses_radiolist
 
     current = _get_current_memory_provider()
     providers = _discover_memory_providers()
@@ -838,7 +838,7 @@ def _configure_memory_provider() -> bool:
 
 def _configure_context_engine() -> bool:
     """Launch a radio picker for context engines. Returns True if changed."""
-    from hermes_cli.curses_ui import curses_radiolist
+    from hermes_agent.cli.ui.curses import curses_radiolist
 
     current = _get_current_context_engine()
     engines = _discover_context_engines()
@@ -938,7 +938,7 @@ def cmd_toggle() -> None:
 def _run_composite_ui(curses, plugin_names, plugin_labels, plugin_selected,
                       disabled, categories, console):
     """Custom curses screen with checkboxes + category action rows."""
-    from hermes_cli.curses_ui import flush_stdin
+    from hermes_agent.cli.ui.curses import flush_stdin
 
     chosen = set(plugin_selected)
     n_plugins = len(plugin_names)
@@ -1188,7 +1188,7 @@ def _run_composite_ui(curses, plugin_names, plugin_labels, plugin_selected,
 def _run_composite_fallback(plugin_names, plugin_labels, plugin_selected,
                             disabled, categories, console):
     """Text-based fallback for the composite plugins UI."""
-    from hermes_cli.colors import Colors, color
+    from hermes_agent.cli.ui.colors import Colors, color
 
     print(color("\n  Plugins", Colors.YELLOW))
 

hermes_agent/cli/profiles.py

@@ -84,7 +84,7 @@ _DEFAULT_EXPORT_EXCLUDE_ROOT = frozenset({
     "node_modules",         # npm packages
     # Databases & runtime state
     "state.db", "state.db-shm", "state.db-wal",
-    "hermes_state.db",
+    "state.db",
     "response_store.db", "response_store.db-shm", "response_store.db-wal",
     "gateway.pid", "gateway_state.json", "processes.json",
     "auth.json",            # API keys, OAuth tokens, credential pools
@@ -138,7 +138,7 @@ def _get_default_hermes_home() -> Path:
     In Docker/custom deployments where HERMES_HOME is outside ``~/.hermes``
     (e.g. ``/opt/data``), returns HERMES_HOME directly.
     """
-    from hermes_constants import get_default_hermes_root
+    from hermes_agent.constants import get_default_hermes_root
     return get_default_hermes_root()
 
 
@@ -301,7 +301,7 @@ def _read_config_model(profile_dir: Path) -> tuple:
 def _check_gateway_running(profile_dir: Path) -> bool:
     """Check if a gateway is running for a given profile directory."""
     try:
-        from gateway.status import get_running_pid
+        from hermes_agent.gateway.status import get_running_pid
         return get_running_pid(profile_dir / "gateway.pid", cleanup_stale=False) is not None
     except Exception:
         return False
@@ -413,7 +413,7 @@ def create_profile(
     if clone_from is not None or clone_all or clone_config:
         if clone_from is None:
             # Default: clone from active profile
-            from hermes_constants import get_hermes_home
+            from hermes_agent.constants import get_hermes_home
             source_dir = get_hermes_home()
         else:
             validate_profile_name(clone_from)
@@ -455,7 +455,7 @@ def create_profile(
     soul_path = profile_dir / "SOUL.md"
     if not soul_path.exists():
         try:
-            from hermes_cli.default_soul import DEFAULT_SOUL_MD
+            from hermes_agent.cli.default_soul import DEFAULT_SOUL_MD
             soul_path.write_text(DEFAULT_SOUL_MD, encoding="utf-8")
         except Exception:
             pass  # best-effort — don't fail profile creation over this
@@ -469,11 +469,11 @@ def seed_profile_skills(profile_dir: Path, quiet: bool = False) -> Optional[dict
     Uses subprocess because sync_skills() caches HERMES_HOME at module level.
     Returns the sync result dict, or None on failure.
     """
-    project_root = Path(__file__).parent.parent.resolve()
+    project_root = Path(__file__).resolve().parents[2].resolve()
     try:
         result = subprocess.run(
             [sys.executable, "-c",
-             "import json; from tools.skills_sync import sync_skills; "
+             "import json; from hermes_agent.tools.skills.sync import sync_skills; "
              "r = sync_skills(quiet=True); print(json.dumps(r))"],
             env={**os.environ, "HERMES_HOME": str(profile_dir)},
             cwd=str(project_root),
@@ -597,7 +597,7 @@ def _cleanup_gateway_service(name: str, profile_dir: Path) -> None:
     old_home = os.environ.get("HERMES_HOME")
     try:
         os.environ["HERMES_HOME"] = str(profile_dir)
-        from hermes_cli.gateway import get_service_name, get_launchd_plist_path
+        from hermes_agent.cli.gateway import get_service_name, get_launchd_plist_path
 
         if _platform.system() == "Linux":
             svc_name = get_service_name()
@@ -720,7 +720,7 @@ def get_active_profile_name() -> str:
     Returns the profile name if HERMES_HOME points into ``~/.hermes/profiles/<name>``.
     Returns ``"custom"`` if HERMES_HOME is set to an unrecognized path.
     """
-    from hermes_constants import get_hermes_home
+    from hermes_agent.constants import get_hermes_home
     hermes_home = get_hermes_home()
     resolved = hermes_home.resolve()
 

hermes_agent/cli/providers.py

@@ -23,7 +23,7 @@ import logging
 from dataclasses import dataclass
 from typing import Any, Dict, List, Optional, Tuple
 
-from utils import base_url_host_matches, base_url_hostname
+from hermes_agent.utils import base_url_host_matches, base_url_hostname
 
 logger = logging.getLogger(__name__)
 
@@ -341,7 +341,7 @@ def get_provider(name: str) -> Optional[ProviderDef]:
 
     # Try to get models.dev data
     try:
-        from agent.models_dev import get_provider_info as _mdev_provider
+        from hermes_agent.providers.metadata_dev import get_provider_info as _mdev_provider
         mdev_info = _mdev_provider(canonical)
     except Exception:
         mdev_info = None
@@ -596,7 +596,7 @@ def resolve_provider_full(
 
     # 3. Try models.dev directly (for providers not in our ALIASES)
     try:
-        from agent.models_dev import get_provider_info as _mdev_provider
+        from hermes_agent.providers.metadata_dev import get_provider_info as _mdev_provider
         mdev_info = _mdev_provider(canonical)
         if mdev_info is not None:
             return ProviderDef(

hermes_agent/cli/runtime_provider.py

@@ -9,9 +9,9 @@ from typing import Any, Dict, Optional
 
 logger = logging.getLogger(__name__)
 
-from hermes_cli import auth as auth_mod
-from agent.credential_pool import CredentialPool, PooledCredential, get_custom_provider_pool_key, load_pool
-from hermes_cli.auth import (
+from hermes_agent.cli.auth import auth as auth_mod
+from hermes_agent.providers.credential_pool import CredentialPool, PooledCredential, get_custom_provider_pool_key, load_pool
+from hermes_agent.cli.auth.auth import (
     AuthError,
     DEFAULT_CODEX_BASE_URL,
     DEFAULT_QWEN_BASE_URL,
@@ -27,9 +27,9 @@ from hermes_cli.auth import (
     resolve_external_process_provider_credentials,
     has_usable_secret,
 )
-from hermes_cli.config import get_compatible_custom_providers, load_config
-from hermes_constants import OPENROUTER_BASE_URL
-from utils import base_url_host_matches, base_url_hostname
+from hermes_agent.cli.config import get_compatible_custom_providers, load_config
+from hermes_agent.constants import OPENROUTER_BASE_URL
+from hermes_agent.utils import base_url_host_matches, base_url_hostname
 
 
 def _normalize_custom_provider_name(value: str) -> str:
@@ -134,7 +134,7 @@ def _copilot_runtime_api_mode(model_cfg: Dict[str, Any], api_key: str) -> str:
         return "chat_completions"
 
     try:
-        from hermes_cli.models import copilot_model_api_mode
+        from hermes_agent.cli.models.models import copilot_model_api_mode
 
         return copilot_model_api_mode(model_name, api_key=api_key)
     except Exception:
@@ -206,7 +206,7 @@ def _resolve_runtime_from_pool_entry(
         if configured_mode and _provider_supports_explicit_api_mode(provider, configured_provider):
             api_mode = configured_mode
         elif provider in ("opencode-zen", "opencode-go"):
-            from hermes_cli.models import opencode_model_api_mode
+            from hermes_agent.cli.models.models import opencode_model_api_mode
             api_mode = opencode_model_api_mode(provider, model_cfg.get("default", ""))
         else:
             # Auto-detect Anthropic-compatible endpoints (/anthropic suffix,
@@ -567,7 +567,7 @@ def _resolve_explicit_runtime(
         base_url = explicit_base_url or cfg_base_url or "https://api.anthropic.com"
         api_key = explicit_api_key
         if not api_key:
-            from agent.anthropic_adapter import resolve_anthropic_token
+            from hermes_agent.providers.anthropic_adapter import resolve_anthropic_token
 
             api_key = resolve_anthropic_token()
             if not api_key:
@@ -870,7 +870,7 @@ def resolve_runtime_provider(
 
     # Anthropic (native Messages API)
     if provider == "anthropic":
-        from agent.anthropic_adapter import resolve_anthropic_token
+        from hermes_agent.providers.anthropic_adapter import resolve_anthropic_token
         token = resolve_anthropic_token()
         if not token:
             raise AuthError(
@@ -896,7 +896,7 @@ def resolve_runtime_provider(
 
     # AWS Bedrock (native Converse API via boto3)
     if provider == "bedrock":
-        from agent.bedrock_adapter import (
+        from hermes_agent.providers.bedrock_adapter import (
             has_aws_credentials,
             resolve_aws_auth_env_var,
             resolve_bedrock_region,
@@ -989,7 +989,7 @@ def resolve_runtime_provider(
             if configured_mode and _provider_supports_explicit_api_mode(provider, configured_provider):
                 api_mode = configured_mode
             elif provider in ("opencode-zen", "opencode-go"):
-                from hermes_cli.models import opencode_model_api_mode
+                from hermes_agent.cli.models.models import opencode_model_api_mode
                 api_mode = opencode_model_api_mode(provider, model_cfg.get("default", ""))
             else:
                 # Auto-detect Anthropic-compatible endpoints by URL convention

hermes_agent/cli/setup_wizard.py

@@ -20,14 +20,14 @@ import copy
 from pathlib import Path
 from typing import Optional, Dict, Any
 
-from hermes_cli.nous_subscription import get_nous_subscription_features
-from tools.tool_backend_helpers import managed_nous_tools_enabled
-from utils import base_url_hostname
-from hermes_constants import get_optional_skills_dir
+from hermes_agent.cli.nous_subscription import get_nous_subscription_features
+from hermes_agent.tools.backend_helpers import managed_nous_tools_enabled
+from hermes_agent.utils import base_url_hostname
+from hermes_agent.constants import get_optional_skills_dir
 
 logger = logging.getLogger(__name__)
 
-PROJECT_ROOT = Path(__file__).parent.parent.resolve()
+PROJECT_ROOT = Path(__file__).resolve().parents[2].resolve()
 
 _DOCS_BASE = "https://hermes-agent.nousresearch.com/docs"
 
@@ -59,7 +59,7 @@ def _supports_same_provider_pool_setup(provider: str) -> bool:
         return False
     if provider == "openrouter":
         return True
-    from hermes_cli.auth import PROVIDER_REGISTRY
+    from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
 
     pconfig = PROVIDER_REGISTRY.get(provider)
     if not pconfig:
@@ -129,7 +129,7 @@ def _set_reasoning_effort(config: Dict[str, Any], effort: str) -> None:
 
 
 # Import config helpers
-from hermes_cli.config import (
+from hermes_agent.cli.config import (
     DEFAULT_CONFIG,
     get_hermes_home,
     get_config_path,
@@ -142,7 +142,7 @@ from hermes_cli.config import (
 )
 # display_hermes_home imported lazily at call sites (stale-module safety during hermes update)
 
-from hermes_cli.colors import Colors, color
+from hermes_agent.cli.ui.colors import Colors, color
 
 
 def print_header(title: str):
@@ -151,7 +151,7 @@ def print_header(title: str):
     print(color(f"◆ {title}", Colors.CYAN, Colors.BOLD))
 
 
-from hermes_cli.cli_output import (  # noqa: E402
+from hermes_agent.cli.ui.output import (  # noqa: E402
     print_error,
     print_info,
     print_success,
@@ -212,7 +212,7 @@ def prompt(question: str, default: str = None, password: bool = False) -> str:
 
 def _curses_prompt_choice(question: str, choices: list, default: int = 0, description: str | None = None) -> int:
     """Single-select menu using curses. Delegates to curses_radiolist."""
-    from hermes_cli.curses_ui import curses_radiolist
+    from hermes_agent.cli.ui.curses import curses_radiolist
     return curses_radiolist(question, choices, selected=default, cancel_returns=-1, description=description)
 
 
@@ -302,7 +302,7 @@ def prompt_checklist(title: str, items: list, pre_selected: list = None) -> list
     if pre_selected is None:
         pre_selected = []
 
-    from hermes_cli.curses_ui import curses_checklist
+    from hermes_agent.cli.ui.curses import curses_checklist
 
     chosen = curses_checklist(
         title,
@@ -352,7 +352,7 @@ def _print_setup_summary(config: dict, hermes_home):
 
     # Vision — use the same runtime resolver as the actual vision tools
     try:
-        from agent.auxiliary_client import get_available_vision_backends
+        from hermes_agent.providers.auxiliary import get_available_vision_backends
 
         _vision_backends = get_available_vision_backends()
     except Exception:
@@ -419,8 +419,8 @@ def _print_setup_summary(config: dict, hermes_home):
         # setups don't show as "missing FAL_KEY".
         _img_backend = None
         try:
-            from agent.image_gen_registry import list_providers
-            from hermes_cli.plugins import _ensure_plugins_discovered
+            from hermes_agent.agent.image_gen.registry import list_providers
+            from hermes_agent.cli.plugins import _ensure_plugins_discovered
 
             _ensure_plugins_discovered()
             for _p in list_providers():
@@ -536,7 +536,7 @@ def _print_setup_summary(config: dict, hermes_home):
         print_warning(
             "Some tools are disabled. Run 'hermes setup tools' to configure them,"
         )
-        from hermes_constants import display_hermes_home as _dhh
+        from hermes_agent.constants import display_hermes_home as _dhh
         print_warning(f"or edit {_dhh()}/.env directly to add the missing API keys.")
         print()
 
@@ -560,7 +560,7 @@ def _print_setup_summary(config: dict, hermes_home):
     print()
 
     # Show file locations prominently
-    from hermes_constants import display_hermes_home as _dhh
+    from hermes_agent.constants import display_hermes_home as _dhh
     print(color(f"📁 All your files are in {_dhh()}/:", Colors.CYAN, Colors.BOLD))
     print()
     print(f"   {color('Settings:', Colors.YELLOW)}  {get_config_path()}")
@@ -665,7 +665,7 @@ def setup_model_provider(config: dict, *, quick: bool = False):
     When *quick* is True, skips credential rotation, vision, and TTS
     configuration — used by the streamlined first-time quick setup.
     """
-    from hermes_cli.config import load_config, save_config
+    from hermes_agent.cli.config import load_config, save_config
 
     print_header("Inference Provider")
     print_info("Choose how to connect to your main chat model.")
@@ -674,7 +674,7 @@ def setup_model_provider(config: dict, *, quick: bool = False):
 
     # Delegate to the shared hermes model flow — handles provider picker,
     # credential prompting, model selection, and config persistence.
-    from hermes_cli.main import select_provider_and_model
+    from hermes_agent.cli.main import select_provider_and_model
     try:
         select_provider_and_model()
     except (SystemExit, KeyboardInterrupt):
@@ -708,8 +708,8 @@ def setup_model_provider(config: dict, *, quick: bool = False):
     if not quick and _supports_same_provider_pool_setup(selected_provider):
         try:
             from types import SimpleNamespace
-            from agent.credential_pool import load_pool
-            from hermes_cli.auth_commands import auth_add_command
+            from hermes_agent.providers.credential_pool import load_pool
+            from hermes_agent.cli.auth.commands import auth_add_command
 
             pool = load_pool(selected_provider)
             entries = pool.entries()
@@ -786,7 +786,7 @@ def setup_model_provider(config: dict, *, quick: bool = False):
         _vision_needs_setup = False
     else:
         try:
-            from agent.auxiliary_client import get_available_vision_backends
+            from hermes_agent.providers.auxiliary import get_available_vision_backends
             _vision_backends = set(get_available_vision_backends())
         except Exception:
             _vision_backends = set()
@@ -1075,7 +1075,7 @@ def _setup_tts_provider(config: dict):
                 save_env_value("XAI_API_KEY", api_key)
                 print_success("xAI TTS API key saved")
             else:
-                from hermes_constants import display_hermes_home as _dhh
+                from hermes_agent.constants import display_hermes_home as _dhh
                 print_warning(
                     "No xAI API key provided for TTS. Configure XAI_API_KEY via "
                     f"hermes setup model or {_dhh()}/.env to use xAI TTS. "
@@ -1284,8 +1284,8 @@ def setup_terminal_backend(config: dict):
     elif selected_backend == "modal":
         print_success("Terminal backend: Modal")
         print_info("Serverless cloud sandboxes. Each session gets its own container.")
-        from tools.managed_tool_gateway import is_managed_tool_gateway_ready
-        from tools.tool_backend_helpers import normalize_modal_mode
+        from hermes_agent.tools.managed_gateway import is_managed_tool_gateway_ready
+        from hermes_agent.tools.backend_helpers import normalize_modal_mode
 
         managed_modal_available = bool(
             managed_nous_tools_enabled()
@@ -2040,49 +2040,49 @@ def _setup_whatsapp():
 
 def _setup_weixin():
     """Configure Weixin (personal WeChat) via iLink Bot API QR login."""
-    from hermes_cli.gateway import _setup_weixin as _gateway_setup_weixin
+    from hermes_agent.cli.gateway import _setup_weixin as _gateway_setup_weixin
     _gateway_setup_weixin()
 
 
 def _setup_signal():
     """Configure Signal via gateway setup."""
-    from hermes_cli.gateway import _setup_signal as _gateway_setup_signal
+    from hermes_agent.cli.gateway import _setup_signal as _gateway_setup_signal
     _gateway_setup_signal()
 
 
 def _setup_email():
     """Configure Email via gateway setup."""
-    from hermes_cli.gateway import _setup_email as _gateway_setup_email
+    from hermes_agent.cli.gateway import _setup_email as _gateway_setup_email
     _gateway_setup_email()
 
 
 def _setup_sms():
     """Configure SMS (Twilio) via gateway setup."""
-    from hermes_cli.gateway import _setup_sms as _gateway_setup_sms
+    from hermes_agent.cli.gateway import _setup_sms as _gateway_setup_sms
     _gateway_setup_sms()
 
 
 def _setup_dingtalk():
     """Configure DingTalk via gateway setup."""
-    from hermes_cli.gateway import _setup_dingtalk as _gateway_setup_dingtalk
+    from hermes_agent.cli.gateway import _setup_dingtalk as _gateway_setup_dingtalk
     _gateway_setup_dingtalk()
 
 
 def _setup_feishu():
     """Configure Feishu / Lark via gateway setup."""
-    from hermes_cli.gateway import _setup_feishu as _gateway_setup_feishu
+    from hermes_agent.cli.gateway import _setup_feishu as _gateway_setup_feishu
     _gateway_setup_feishu()
 
 
 def _setup_wecom():
     """Configure WeCom (Enterprise WeChat) via gateway setup."""
-    from hermes_cli.gateway import _setup_wecom as _gateway_setup_wecom
+    from hermes_agent.cli.gateway import _setup_wecom as _gateway_setup_wecom
     _gateway_setup_wecom()
 
 
 def _setup_wecom_callback():
     """Configure WeCom Callback (self-built app) via gateway setup."""
-    from hermes_cli.gateway import _setup_wecom_callback as _gw_setup
+    from hermes_agent.cli.gateway import _setup_wecom_callback as _gw_setup
     _gw_setup()
 
 
@@ -2155,7 +2155,7 @@ def _setup_bluebubbles():
 
 def _setup_qqbot():
     """Configure QQ Bot (Official API v2) via gateway setup."""
-    from hermes_cli.gateway import _setup_qqbot as _gateway_setup_qqbot
+    from hermes_agent.cli.gateway import _setup_qqbot as _gateway_setup_qqbot
     _gateway_setup_qqbot()
 
 
@@ -2194,7 +2194,7 @@ def _setup_webhooks():
     save_env_value("WEBHOOK_ENABLED", "true")
     print()
     print_success("Webhooks enabled! Next steps:")
-    from hermes_constants import display_hermes_home as _dhh
+    from hermes_agent.constants import display_hermes_home as _dhh
     print_info(f"   1. Define webhook routes in {_dhh()}/config.yaml")
     print_info("   2. Point your service (GitHub, GitLab, etc.) at:")
     print_info("      http://your-server:8644/webhooks/<route-name>")
@@ -2318,7 +2318,7 @@ def setup_gateway(config: dict):
         _is_linux = _platform.system() == "Linux"
         _is_macos = _platform.system() == "Darwin"
 
-        from hermes_cli.gateway import (
+        from hermes_agent.cli.gateway import (
             _is_service_installed,
             _is_service_running,
             supports_systemd_services,
@@ -2398,7 +2398,7 @@ def setup_gateway(config: dict):
                     print_info("  Or as a boot-time service: sudo hermes gateway install --system")
                 print_info("  Or run in foreground:  hermes gateway")
         else:
-            from hermes_constants import is_container
+            from hermes_agent.constants import is_container
             if is_container():
                 print_info("Start the gateway to bring your bots online:")
                 print_info("   hermes gateway run          # Run as container main process")
@@ -2428,7 +2428,7 @@ def setup_tools(config: dict, first_install: bool = False):
         first_install: When True, uses the simplified first-install flow
             (no platform menu, prompts for all unconfigured API keys).
     """
-    from hermes_cli.tools_config import tools_command
+    from hermes_agent.cli.tools_config import tools_command
 
     tools_command(first_install=first_install, config=config)
 
@@ -2450,14 +2450,14 @@ def _model_section_has_credentials(config: dict) -> bool:
         ``OPENAI_API_KEY`` / ``OPENROUTER_API_KEY`` values through OpenRouter.
     """
     try:
-        from hermes_cli.auth import get_active_provider
+        from hermes_agent.cli.auth.auth import get_active_provider
         if get_active_provider():
             return True
     except Exception:
         pass
 
     try:
-        from hermes_cli.auth import PROVIDER_REGISTRY
+        from hermes_agent.cli.auth.auth import PROVIDER_REGISTRY
     except Exception:
         PROVIDER_REGISTRY = {}  # type: ignore[assignment]
 
@@ -2863,7 +2863,7 @@ def run_setup_wizard(args):
       hermes setup tools     — just tool configuration
       hermes setup agent     — just agent settings
     """
-    from hermes_cli.config import is_managed, managed_error
+    from hermes_agent.cli.config import is_managed, managed_error
     if is_managed():
         managed_error("run setup wizard")
         return
@@ -2918,7 +2918,7 @@ def run_setup_wizard(args):
         return
 
     # Check if this is an existing installation with a provider configured
-    from hermes_cli.auth import get_active_provider
+    from hermes_agent.cli.auth.auth import get_active_provider
 
     active_provider = get_active_provider()
     is_existing = (
@@ -3072,8 +3072,8 @@ def _resolve_hermes_chat_argv() -> Optional[list[str]]:
         return [hermes_bin, "chat"]
 
     try:
-        if importlib.util.find_spec("hermes_cli") is not None:
-            return [sys.executable, "-m", "hermes_cli.main", "chat"]
+        if importlib.util.find_spec("hermes_agent.cli") is not None:
+            return [sys.executable, "-m", "hermes_agent.cli.main", "chat"]
     except Exception:
         pass
 
@@ -3140,7 +3140,7 @@ def _run_first_time_quick_setup(config: dict, hermes_home, is_existing: bool):
 
 def _run_quick_setup(config: dict, hermes_home):
     """Quick setup — only configure items that are missing."""
-    from hermes_cli.config import (
+    from hermes_agent.cli.config import (
         get_missing_env_vars,
         get_missing_config_fields,
         check_config_version,

hermes_agent/cli/skills_config.py

@@ -13,9 +13,9 @@ Config stored in ~/.hermes/config.yaml under:
 """
 from typing import List, Optional, Set
 
-from hermes_cli.config import load_config, save_config
-from hermes_cli.colors import Colors, color
-from hermes_cli.platforms import PLATFORMS as _PLATFORMS
+from hermes_agent.cli.config import load_config, save_config
+from hermes_agent.cli.ui.colors import Colors, color
+from hermes_agent.cli.platforms import PLATFORMS as _PLATFORMS
 
 # Backward-compatible view: {key: label_string} so existing code that
 # iterates ``PLATFORMS.items()`` or calls ``PLATFORMS.get(key)`` keeps
@@ -52,7 +52,7 @@ def save_disabled_skills(config: dict, disabled: Set[str], platform: Optional[st
 def _list_all_skills() -> List[dict]:
     """Return all installed skills (ignoring disabled state)."""
     try:
-        from tools.skills_tool import _find_all_skills
+        from hermes_agent.tools.skills.tool import _find_all_skills
         return _find_all_skills(skip_disabled=True)
     except Exception:
         return []
@@ -93,7 +93,7 @@ def _select_platform() -> Optional[str]:
 
 def _toggle_by_category(skills: List[dict], disabled: Set[str]) -> Set[str]:
     """Toggle all skills in a category at once."""
-    from hermes_cli.curses_ui import curses_checklist
+    from hermes_agent.cli.ui.curses import curses_checklist
 
     categories = _get_categories(skills)
     cat_labels = []
@@ -124,7 +124,7 @@ def _toggle_by_category(skills: List[dict], disabled: Set[str]) -> Set[str]:
 
 def skills_command(args=None):
     """Entry point for `hermes skills`."""
-    from hermes_cli.curses_ui import curses_checklist
+    from hermes_agent.cli.ui.curses import curses_checklist
 
     config = load_config()
     skills = _list_all_skills()

hermes_agent/cli/skills_hub.py

@@ -21,7 +21,7 @@ from rich.table import Table
 
 # Lazy imports to avoid circular dependencies and slow startup.
 # tools.skills_hub and tools.skills_guard are imported inside functions.
-from hermes_constants import display_hermes_home
+from hermes_agent.constants import display_hermes_home
 
 _console = Console()
 
@@ -37,7 +37,7 @@ def _resolve_short_name(name: str, sources, console: Console) -> str:
     matches exist, shows them and asks the user to use the full identifier.
     Returns empty string if nothing found or ambiguous.
     """
-    from tools.skills_hub import unified_search
+    from hermes_agent.tools.skills.hub import unified_search
 
     c = console or _console
     c.print(f"[dim]Resolving '{name}'...[/]")
@@ -144,7 +144,7 @@ def _derive_category_from_install_path(install_path: str) -> str:
 def do_search(query: str, source: str = "all", limit: int = 10,
               console: Optional[Console] = None) -> None:
     """Search registries and display results as a Rich table."""
-    from tools.skills_hub import GitHubAuth, create_source_router, unified_search
+    from hermes_agent.tools.skills.hub import GitHubAuth, create_source_router, unified_search
 
     c = console or _console
     c.print(f"\n[bold]Searching for:[/] {query}")
@@ -187,7 +187,7 @@ def do_browse(page: int = 1, page_size: int = 20, source: str = "all",
 
     Official skills are always shown first, regardless of source filter.
     """
-    from tools.skills_hub import (
+    from hermes_agent.tools.skills.hub import (
         GitHubAuth, create_source_router, parallel_search_sources,
     )
 
@@ -311,11 +311,11 @@ def do_install(identifier: str, category: str = "", force: bool = False,
                console: Optional[Console] = None, skip_confirm: bool = False,
                invalidate_cache: bool = True) -> None:
     """Fetch, quarantine, scan, confirm, and install a skill."""
-    from tools.skills_hub import (
+    from hermes_agent.tools.skills.hub import (
         GitHubAuth, create_source_router, ensure_hub_dirs,
         quarantine_bundle, install_from_quarantine, HubLockFile,
     )
-    from tools.skills_guard import scan_skill, should_allow_install, format_scan_report
+    from hermes_agent.tools.skills.guard import scan_skill, should_allow_install, format_scan_report
 
     c = console or _console
     ensure_hub_dirs()
@@ -377,7 +377,7 @@ def do_install(identifier: str, category: str = "", force: bool = False,
         q_path = quarantine_bundle(bundle)
     except ValueError as exc:
         c.print(f"[bold red]Installation blocked:[/] {exc}\n")
-        from tools.skills_hub import append_audit_log
+        from hermes_agent.tools.skills.hub import append_audit_log
         append_audit_log("BLOCKED", bundle.name, bundle.source,
                          bundle.trust_level, "invalid_path", str(exc))
         return
@@ -395,7 +395,7 @@ def do_install(identifier: str, category: str = "", force: bool = False,
         c.print(f"\n[bold red]Installation blocked:[/] {reason}")
         # Clean up quarantine
         shutil.rmtree(q_path, ignore_errors=True)
-        from tools.skills_hub import append_audit_log
+        from hermes_agent.tools.skills.hub import append_audit_log
         append_audit_log("BLOCKED", bundle.name, bundle.source,
                          bundle.trust_level, result.verdict,
                          f"{len(result.findings)}_findings")
@@ -445,18 +445,18 @@ def do_install(identifier: str, category: str = "", force: bool = False,
     except ValueError as exc:
         c.print(f"[bold red]Installation blocked:[/] {exc}\n")
         shutil.rmtree(q_path, ignore_errors=True)
-        from tools.skills_hub import append_audit_log
+        from hermes_agent.tools.skills.hub import append_audit_log
         append_audit_log("BLOCKED", bundle.name, bundle.source,
                          bundle.trust_level, "invalid_path", str(exc))
         return
-    from tools.skills_hub import SKILLS_DIR
+    from hermes_agent.tools.skills.hub import SKILLS_DIR
     c.print(f"[bold green]Installed:[/] {install_dir.relative_to(SKILLS_DIR)}")
     c.print(f"[dim]Files: {', '.join(bundle.files.keys())}[/]\n")
 
     if invalidate_cache:
         # Invalidate the skills prompt cache so the new skill appears immediately
         try:
-            from agent.prompt_builder import clear_skills_system_prompt_cache
+            from hermes_agent.agent.prompt_builder import clear_skills_system_prompt_cache
             clear_skills_system_prompt_cache(clear_snapshot=True)
         except Exception:
             pass
@@ -467,7 +467,7 @@ def do_install(identifier: str, category: str = "", force: bool = False,
 
 def do_inspect(identifier: str, console: Optional[Console] = None) -> None:
     """Preview a skill's SKILL.md content without installing."""
-    from tools.skills_hub import GitHubAuth, create_source_router
+    from hermes_agent.tools.skills.hub import GitHubAuth, create_source_router
 
     c = console or _console
     auth = GitHubAuth()
@@ -520,7 +520,7 @@ def browse_skills(page: int = 1, page_size: int = 20, source: str = "all") -> di
 
     Returns ``{"items": [...], "page": int, "total_pages": int, "total": int}``.
     """
-    from tools.skills_hub import GitHubAuth, create_source_router
+    from hermes_agent.tools.skills.hub import GitHubAuth, create_source_router
 
     page_size = max(1, min(page_size, 100))
     _TRUST_RANK = {"builtin": 3, "trusted": 2, "community": 1}
@@ -563,7 +563,7 @@ def browse_skills(page: int = 1, page_size: int = 20, source: str = "all") -> di
 
 def inspect_skill(identifier: str) -> Optional[dict]:
     """Skill metadata (+ SKILL.md preview) for programmatic callers."""
-    from tools.skills_hub import GitHubAuth, create_source_router
+    from hermes_agent.tools.skills.hub import GitHubAuth, create_source_router
 
     class _Q:
         def print(self, *a, **k):
@@ -601,9 +601,9 @@ def inspect_skill(identifier: str) -> Optional[dict]:
 
 def do_list(source_filter: str = "all", console: Optional[Console] = None) -> None:
     """List installed skills, distinguishing hub, builtin, and local skills."""
-    from tools.skills_hub import HubLockFile, ensure_hub_dirs
-    from tools.skills_sync import _read_manifest
-    from tools.skills_tool import _find_all_skills
+    from hermes_agent.tools.skills.hub import HubLockFile, ensure_hub_dirs
+    from hermes_agent.tools.skills.sync import _read_manifest
+    from hermes_agent.tools.skills.tool import _find_all_skills
 
     c = console or _console
     ensure_hub_dirs()
@@ -659,7 +659,7 @@ def do_list(source_filter: str = "all", console: Optional[Console] = None) -> No
 
 def do_check(name: Optional[str] = None, console: Optional[Console] = None) -> None:
     """Check hub-installed skills for upstream updates."""
-    from tools.skills_hub import check_for_skill_updates
+    from hermes_agent.tools.skills.hub import check_for_skill_updates
 
     c = console or _console
     results = check_for_skill_updates(name=name)
@@ -682,7 +682,7 @@ def do_check(name: Optional[str] = None, console: Optional[Console] = None) -> N
 
 def do_update(name: Optional[str] = None, console: Optional[Console] = None) -> None:
     """Update hub-installed skills with upstream changes."""
-    from tools.skills_hub import HubLockFile, check_for_skill_updates
+    from hermes_agent.tools.skills.hub import HubLockFile, check_for_skill_updates
 
     c = console or _console
     lock = HubLockFile()
@@ -702,8 +702,8 @@ def do_update(name: Optional[str] = None, console: Optional[Console] = None) ->
 
 def do_audit(name: Optional[str] = None, console: Optional[Console] = None) -> None:
     """Re-run security scan on installed hub skills."""
-    from tools.skills_hub import HubLockFile, SKILLS_DIR
-    from tools.skills_guard import scan_skill, format_scan_report
+    from hermes_agent.tools.skills.hub import HubLockFile, SKILLS_DIR
+    from hermes_agent.tools.skills.guard import scan_skill, format_scan_report
 
     c = console or _console
     lock = HubLockFile()
@@ -737,7 +737,7 @@ def do_uninstall(name: str, console: Optional[Console] = None,
                  skip_confirm: bool = False,
                  invalidate_cache: bool = True) -> None:
     """Remove a hub-installed skill with confirmation."""
-    from tools.skills_hub import uninstall_skill
+    from hermes_agent.tools.skills.hub import uninstall_skill
 
     c = console or _console
 
@@ -757,7 +757,7 @@ def do_uninstall(name: str, console: Optional[Console] = None,
         c.print(f"[bold green]{msg}[/]\n")
         if invalidate_cache:
             try:
-                from agent.prompt_builder import clear_skills_system_prompt_cache
+                from hermes_agent.agent.prompt_builder import clear_skills_system_prompt_cache
                 clear_skills_system_prompt_cache(clear_snapshot=True)
             except Exception:
                 pass
@@ -773,7 +773,7 @@ def do_reset(name: str, restore: bool = False,
              skip_confirm: bool = False,
              invalidate_cache: bool = True) -> None:
     """Reset a bundled skill's manifest tracking (+ optionally restore from bundled)."""
-    from tools.skills_sync import reset_bundled_skill
+    from hermes_agent.tools.skills.sync import reset_bundled_skill
 
     c = console or _console
 
@@ -804,7 +804,7 @@ def do_reset(name: str, restore: bool = False,
 
     if invalidate_cache:
         try:
-            from agent.prompt_builder import clear_skills_system_prompt_cache
+            from hermes_agent.agent.prompt_builder import clear_skills_system_prompt_cache
             clear_skills_system_prompt_cache(clear_snapshot=True)
         except Exception:
             pass
@@ -815,7 +815,7 @@ def do_reset(name: str, restore: bool = False,
 
 def do_tap(action: str, repo: str = "", console: Optional[Console] = None) -> None:
     """Manage taps (custom GitHub repo sources)."""
-    from tools.skills_hub import TapsManager
+    from hermes_agent.tools.skills.hub import TapsManager
 
     c = console or _console
     mgr = TapsManager()
@@ -859,8 +859,8 @@ def do_tap(action: str, repo: str = "", console: Optional[Console] = None) -> No
 def do_publish(skill_path: str, target: str = "github", repo: str = "",
                console: Optional[Console] = None) -> None:
     """Publish a local skill to a registry (GitHub PR or ClawHub submission)."""
-    from tools.skills_hub import GitHubAuth, SKILLS_DIR
-    from tools.skills_guard import scan_skill, format_scan_report
+    from hermes_agent.tools.skills.hub import GitHubAuth, SKILLS_DIR
+    from hermes_agent.tools.skills.guard import scan_skill, format_scan_report
 
     c = console or _console
     path = Path(skill_path)
@@ -1024,7 +1024,7 @@ def _github_publish(skill_path: Path, skill_name: str, target_repo: str,
 
 def do_snapshot_export(output_path: str, console: Optional[Console] = None) -> None:
     """Export current hub skill configuration to a portable JSON file."""
-    from tools.skills_hub import HubLockFile, TapsManager
+    from hermes_agent.tools.skills.hub import HubLockFile, TapsManager
 
     c = console or _console
     lock = HubLockFile()
@@ -1065,7 +1065,7 @@ def do_snapshot_export(output_path: str, console: Optional[Console] = None) -> N
 def do_snapshot_import(input_path: str, force: bool = False,
                        console: Optional[Console] = None) -> None:
     """Re-install skills from a snapshot file."""
-    from tools.skills_hub import TapsManager
+    from hermes_agent.tools.skills.hub import TapsManager
 
     c = console or _console
     inp = Path(input_path)

hermes_agent/cli/timeouts.py

@@ -19,7 +19,7 @@ def get_provider_request_timeout(
         return None
 
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
     except ImportError:
         return None
 
@@ -48,7 +48,7 @@ def get_provider_stale_timeout(
         return None
 
     try:
-        from hermes_cli.config import load_config
+        from hermes_agent.cli.config import load_config
     except ImportError:
         return None