fix(installer): heal off-PATH node on update/migration + harden node discovery

Follow-up to the FHS root-install node-PATH fix, addressing the high-risk
gaps a reviewer flagged: fresh-install passing does not mean an existing
broken install gets healed.

Migration repair (the #1 trap):
- node-bootstrap.sh ensure_node() and install.sh check_node() both
  early-returned when a bundled node already existed at HERMES_HOME/node/bin,
  only fixing the current shell PATH and never re-creating the /usr/local/bin
  symlinks. A previously-broken root box therefore stayed broken after
  `hermes update` / re-install.
- Both paths now call a shared link_bundled_node / _nb_link_bundled_node that
  idempotently re-creates the symlinks in the canonical command-link dir AND
  prunes stale links left in the other candidate dirs, so a migrated root
  install no longer keeps shadowing copies in ~/.local/bin (the #34536
  nvm-shadow class).

Parity (messy-middle edge case):
- _nb_get_link_dir() now mirrors resolve_install_layout()'s legacy-install
  carve-out: a root user with HERMES_HOME/hermes-agent/.git keeps ~/.local/bin,
  so the bootstrap path can no longer link node to a different dir than the
  installer placed the hermes command.

Canonical helper (kills the duplicated layout-logic root cause):
- hermes_constants now owns command_link_dir, command_link_display_dir,
  command_link_candidate_dirs, bundled_node_bin_dir, find_node_executable.
  doctor.py, profiles.py, uninstall.py, backup.py, main.py all consume it.

Doctor now catches this class of regression:
- new _resolve_node_for_doctor reports "Node.js installed but not on PATH"
  instead of a false "not found", verifies the /usr/local/bin symlink on
  root FHS, self-heals PATH for the rest of the run, and the npm-audit block
  no longer silently vanishes when npm is off-PATH.
- doctor command-link detection uses the canonical helper, so it no longer
  looks in ~/.local/bin on root FHS or creates a wrong duplicate symlink
  with --fix.

Profile-alias wrappers now land in the layout-aware dir (was hardcoded
~/.local/bin, off-PATH for root FHS); remove_wrapper_script and uninstall
scan all candidate dirs.

Defensive bundled-node fallback (find_node_executable) added to the dashboard
web-UI build, WhatsApp bridge, and LSP installer so an off-PATH bundled node
does not silently disable those features.

Tests: 9 new hermes_constants helper tests + 4 profiles wrapper-dir tests.
Verified on a throwaway VM: fresh-root install (node on PATH, dashboard
serves HTTP 200, tsc present) and the migration scenario (broken old layout
re-installed -> node restored to /usr/local/bin, stale ~/.local/bin pruned).

agent/lsp/install.py

@@ -245,6 +245,14 @@ def _install_npm(
     needs ``typescript`` next to it; intelephense ships standalone).
     """
     npm = shutil.which("npm")
+    if npm is None:
+        # Fall back to the bundled npm at <HERMES_HOME>/node/bin when off-PATH
+        # (e.g. root FHS install whose symlink is missing, #38889).
+        try:
+            from hermes_constants import find_node_executable
+            npm = find_node_executable("npm")
+        except Exception:
+            npm = None
     if npm is None:
         logger.info("[install] cannot install %s: npm not on PATH", pkg)
         return None

gateway/platforms/whatsapp.py

@@ -197,10 +197,15 @@ def check_whatsapp_requirements() -> bool:
     
     WhatsApp requires a Node.js bridge for most implementations.
     """
-    # Check for Node.js.  Resolve via shutil.which so we respect PATHEXT
-    # (node.exe vs node) and get a meaningful "not installed" signal
-    # instead of spawning a cmd flash on Windows.
-    _node = shutil.which("node")
+    # Check for Node.js.  Resolve with bundled-fallback awareness (PATH first,
+    # then <HERMES_HOME>/node/bin) so a bundled-but-off-PATH install (e.g. a
+    # root FHS install whose symlink is missing, #38889) doesn't make the
+    # WhatsApp bridge silently unavailable.
+    try:
+        from hermes_constants import find_node_executable
+        _node = find_node_executable("node")
+    except Exception:
+        _node = shutil.which("node")
     if not _node:
         return False
     try:
@@ -592,8 +597,16 @@ class WhatsAppAdapter(BasePlatformAdapter):
                 print(f"[{self.name}] Installing WhatsApp bridge dependencies...")
                 # Resolve npm path so Windows can execute the .cmd shim.
                 # shutil.which honours PATHEXT; on POSIX it returns the
-                # plain executable path.
-                _npm_bin = shutil.which("npm") or "npm"
+                # plain executable path.  Fall back to the bundled npm at
+                # <HERMES_HOME>/node/bin when off-PATH (#38889).
+                _npm_bin = shutil.which("npm")
+                if not _npm_bin:
+                    try:
+                        from hermes_constants import find_node_executable
+                        _npm_bin = find_node_executable("npm")
+                    except Exception:
+                        _npm_bin = None
+                _npm_bin = _npm_bin or "npm"
                 try:
                     # Read timeout from environment variable, default to 300 seconds (5 minutes)
                     # to accommodate slower systems like Unraid NAS

hermes_cli/backup.py

@@ -448,9 +448,10 @@ def run_import(args) -> None:
                     if skipped:
                         print(f"  Profile aliases skipped:  {', '.join(skipped)}")
                     if not _is_wrapper_dir_in_path():
-                        print(f"\n  Note: {_get_wrapper_dir()} is not in your PATH.")
+                        _wd = _get_wrapper_dir()
+                        print(f"\n  Note: {_wd} is not in your PATH.")
                         print('  Add to your shell config (~/.bashrc or ~/.zshrc):')
-                        print('    export PATH="$HOME/.local/bin:$PATH"')
+                        print(f'    export PATH="{_wd}:$PATH"')
             except ImportError:
                 # hermes_cli.profiles might not be available (fresh install)
                 if any(profiles_dir.iterdir()):

hermes_cli/doctor.py

@@ -13,6 +13,11 @@ from pathlib import Path
 from hermes_cli.config import get_project_root, get_hermes_home, get_env_path
 from hermes_cli.env_loader import load_hermes_dotenv
 from hermes_constants import display_hermes_home
+from hermes_constants import (
+    command_link_dir as _command_link_dir,
+    command_link_display_dir as _command_link_display_dir,
+    bundled_node_bin_dir as _bundled_node_bin_dir,
+)
 
 PROJECT_ROOT = get_project_root()
 HERMES_HOME = get_hermes_home()
@@ -198,6 +203,75 @@ def _section(title: str) -> None:
     print(color(f"◆ {title}", Colors.CYAN, Colors.BOLD))
 
 
+def _resolve_node_for_doctor(issues: list) -> str | None:
+    """Resolve Node.js with bundled-fallback awareness and diagnose off-PATH.
+
+    Returns the resolved ``node`` binary path if node is usable from *some*
+    known location, else ``None``.  Emits the appropriate check_ok/check_warn/
+    check_info lines and appends a fix to ``issues`` when node is installed but
+    unreachable via PATH (the PR #38889 class of regression: bundled node lives
+    at ``<HERMES_HOME>/node/bin`` but its PATH symlink is missing or off-PATH).
+
+    Discovery mirrors tools/browser_tool._browser_candidate_path_dirs and
+    hermes_cli/main._ensure_tui_node so doctor's verdict matches what actually
+    runs.  As a side effect, when a bundled node is found off-PATH it is
+    prepended to ``os.environ["PATH"]`` for the remainder of this doctor run so
+    downstream npm/agent-browser checks don't cascade into false negatives.
+    """
+    on_path = _safe_which("node")
+    if on_path:
+        check_ok("Node.js", f"({on_path})")
+        return on_path
+
+    # Not on PATH — is it installed at the bundled location?
+    bundled = _bundled_node_bin_dir() / "node"
+    if bundled.exists() and os.access(bundled, os.X_OK):
+        bin_dir = bundled.parent
+        check_warn(
+            "Node.js installed but not on PATH",
+            f"(found {bundled}, but `node` is not resolvable via PATH)",
+        )
+        # Root FHS installs are supposed to symlink node into /usr/local/bin.
+        # Verify that canonical symlink so doctor catches the exact PR #38889
+        # breakage rather than only the generic PATH miss.
+        try:
+            is_root = hasattr(os, "geteuid") and os.geteuid() == 0
+        except OSError:
+            is_root = False
+        if is_root and sys.platform == "linux":
+            fhs_link = Path("/usr/local/bin/node")
+            if not fhs_link.exists():
+                check_info(
+                    "Root FHS install: node should be linked into /usr/local/bin."
+                )
+                check_info(f"Fix: ln -sf {bundled} /usr/local/bin/node "
+                           f"(and the same for npm, npx)")
+                issues.append(
+                    "Bundled Node.js is off-PATH on a root FHS install — run: "
+                    f"ln -sf {bundled} /usr/local/bin/node "
+                    "(repeat for npm, npx), or re-run the installer"
+                )
+            elif fhs_link.resolve() != bundled.resolve():
+                check_warn(
+                    "/usr/local/bin/node points to the wrong target",
+                    f"(→ {fhs_link.resolve()}, expected {bundled})",
+                )
+                issues.append(
+                    f"Fix stale node symlink: ln -sf {bundled} /usr/local/bin/node"
+                )
+        else:
+            check_info(f"Bundled Node.js exists at {bin_dir} but isn't on PATH.")
+            check_info(f'Fix: export PATH="{bin_dir}:$PATH"  (add to your shell rc)')
+            issues.append(f"Node.js is installed but off-PATH — add {bin_dir} to PATH")
+
+        # Make the rest of the doctor run see this node so npm/agent-browser
+        # checks succeed instead of reporting more false negatives.
+        os.environ["PATH"] = str(bin_dir) + os.pathsep + os.environ.get("PATH", "")
+        return str(bundled)
+
+    return None
+
+
 def _fail_and_issue(text: str, detail: str, fix: str, issues: list[str]) -> None:
     """Emit a check_fail and append the corresponding fix instruction."""
     check_fail(text, detail)
@@ -1185,15 +1259,11 @@ def run_doctor(args):
                 _venv_bin = _candidate
                 break
 
-        # Determine the expected command link directory (mirrors install.sh logic)
-        _prefix = os.environ.get("PREFIX", "")
-        _is_termux_env = bool(os.environ.get("TERMUX_VERSION")) or "com.termux/files/usr" in _prefix
-        if _is_termux_env and _prefix:
-            _cmd_link_dir = Path(_prefix) / "bin"
-            _cmd_link_display = "$PREFIX/bin"
-        else:
-            _cmd_link_dir = Path.home() / ".local" / "bin"
-            _cmd_link_display = "~/.local/bin"
+        # Determine the expected command link directory (canonical helper —
+        # single source of truth shared with scripts/install.sh, so root FHS
+        # installs correctly resolve to /usr/local/bin instead of ~/.local/bin).
+        _cmd_link_dir = _command_link_dir()
+        _cmd_link_display = _command_link_display_dir()
         _cmd_link = _cmd_link_dir / "hermes"
 
         if _venv_bin is None:
@@ -1244,7 +1314,7 @@ def run_doctor(args):
                     if str(_cmd_link_dir) not in _path_dirs:
                         check_warn(
                             f"{_cmd_link_display} is not on your PATH",
-                            "(add it to your shell config: export PATH=\"$HOME/.local/bin:$PATH\")"
+                            f'(add it to your shell config: export PATH="{_cmd_link_dir}:$PATH")'
                         )
                         manual_issues.append(f"Add {_cmd_link_display} to your PATH")
                 else:
@@ -1373,8 +1443,10 @@ def run_doctor(args):
             )
 
     # Node.js + agent-browser (for browser automation tools)
-    if _safe_which("node"):
-        check_ok("Node.js")
+    # Resolve with bundled-fallback awareness so an off-PATH bundled install
+    # is diagnosed as "installed but not on PATH" instead of "not found".
+    _node_resolved = _resolve_node_for_doctor(issues)
+    if _node_resolved:
         # Check if agent-browser is installed
         agent_browser_path = PROJECT_ROOT / "node_modules" / "agent-browser"
         agent_browser_ok = False
@@ -1451,8 +1523,15 @@ def run_doctor(args):
     else:
         check_warn("Node.js not found", "(optional, needed for browser tools)")
     
-    # npm audit for all Node.js packages
+    # npm audit for all Node.js packages.  Use bundled-fallback resolution so a
+    # bundled-but-off-PATH npm is still found (the _resolve_node_for_doctor call
+    # above already prepended the bundled bin dir to PATH for this run, so plain
+    # which usually works now; the explicit fallback is belt-and-suspenders).
     _npm_bin = _safe_which("npm")
+    if not _npm_bin:
+        _bundled_npm = _bundled_node_bin_dir() / "npm"
+        if _bundled_npm.exists() and os.access(_bundled_npm, os.X_OK):
+            _npm_bin = str(_bundled_npm)
     if _npm_bin:
         npm_dirs = [
             (PROJECT_ROOT, "Browser tools (agent-browser)"),

hermes_cli/main.py

@@ -6817,6 +6817,7 @@ def _run_with_idle_timeout(
     *,
     idle_timeout_seconds: int = 180,
     indent: str = "    ",
+    env: dict | None = None,
 ) -> subprocess.CompletedProcess:
     """Run a subprocess that streams output, with an idle-output timeout.
 
@@ -6851,6 +6852,7 @@ def _run_with_idle_timeout(
             encoding="utf-8",
             errors="replace",
             bufsize=1,
+            env=env,
         )
     except OSError as exc:
         # E.g. npm not on PATH between the which() check and now.
@@ -6915,6 +6917,7 @@ def _run_npm_install_deterministic(
     *,
     extra_args: tuple[str, ...] = (),
     capture_output: bool = True,
+    env: dict | None = None,
 ) -> subprocess.CompletedProcess:
     """Run a deterministic npm install that does not mutate ``package-lock.json``.
 
@@ -6936,6 +6939,7 @@ def _run_npm_install_deterministic(
             encoding="utf-8",
             errors="replace",
             check=False,
+            env=env,
         )
         if ci_result.returncode == 0:
             return ci_result
@@ -6950,6 +6954,7 @@ def _run_npm_install_deterministic(
         encoding="utf-8",
         errors="replace",
         check=False,
+        env=env,
     )
 
 
@@ -6981,12 +6986,44 @@ def _build_web_ui(web_dir: Path, *, fatal: bool = False) -> bool:
             encoding = getattr(sys.stdout, "encoding", None) or "ascii"
             print(text.encode(encoding, errors="replace").decode(encoding, errors="replace"))
 
+    # Resolve npm with bundled-fallback awareness: on a root FHS install whose
+    # PATH symlink is missing, or any context with a stripped PATH (systemd
+    # service, RHEL non-login shell), shutil.which("npm") returns None even
+    # though the bundled npm exists at <HERMES_HOME>/node/bin/npm.  See #38889.
     npm = shutil.which("npm")
+    if not npm:
+        try:
+            from hermes_constants import find_node_executable
+            npm = find_node_executable("npm")
+        except Exception:
+            npm = None
     if not npm:
         if fatal:
             _say("Web UI frontend not built and npm is not available.")
             _say("Install Node.js, then run:  cd web && npm install && npm run build")
         return not fatal
+
+    # Ensure the bundled node/bin dir is on PATH for the build subprocesses so
+    # the `npm run build` step (which shells out to tsc / vite from
+    # node_modules/.bin, and those re-invoke `node`) can find node even when the
+    # caller's PATH doesn't include it.
+    _build_env = None
+    try:
+        from hermes_constants import bundled_node_bin_dir
+        _node_bin = bundled_node_bin_dir()
+        if _node_bin.is_dir():
+            _build_env = os.environ.copy()
+            _existing = _build_env.get("PATH", "")
+            if str(_node_bin) not in _existing.split(os.pathsep):
+                _build_env["PATH"] = str(_node_bin) + os.pathsep + _existing
+        # Also fold in the resolved npm's own dir (covers system node installs).
+        _npm_dir = str(Path(npm).resolve().parent)
+        if _build_env is None:
+            _build_env = os.environ.copy()
+        if _npm_dir not in _build_env.get("PATH", "").split(os.pathsep):
+            _build_env["PATH"] = _npm_dir + os.pathsep + _build_env.get("PATH", "")
+    except Exception:
+        _build_env = None
     _say("→ Building web UI...")
 
     def _relay(result: "subprocess.CompletedProcess") -> None:
@@ -7008,6 +7045,7 @@ def _build_web_ui(web_dir: Path, *, fatal: bool = False) -> bool:
         npm,
         _workspace_root(web_dir),
         extra_args=("--silent",),
+        env=_build_env,
     )
     if r1.returncode != 0:
         _say(
@@ -7023,13 +7061,13 @@ def _build_web_ui(web_dir: Path, *, fatal: bool = False) -> bool:
     # users react by rebooting, which leaves the editable install in a
     # half-state. Streaming + idle-kill makes failures observable AND
     # recoverable (the stale-dist fallback below handles the kill path).
-    r2 = _run_with_idle_timeout([npm, "run", "build"], cwd=web_dir)
+    r2 = _run_with_idle_timeout([npm, "run", "build"], cwd=web_dir, env=_build_env)
     if r2.returncode != 0:
         # Retry once after a short delay — covers boot-time races on Windows
         # (antivirus scanning Node.js binaries, npm cache not ready, transient
         # I/O when launched via Scheduled Task at logon). See issue #23817.
         _time.sleep(3)
-        r2 = _run_with_idle_timeout([npm, "run", "build"], cwd=web_dir)
+        r2 = _run_with_idle_timeout([npm, "run", "build"], cwd=web_dir, env=_build_env)
 
     if r2.returncode != 0:
         # _run_with_idle_timeout merges stderr into stdout; older callers
@@ -11384,11 +11422,12 @@ def cmd_profile(args):
                     if wrapper_path:
                         print(f"Wrapper created: {wrapper_path}")
                         if not _is_wrapper_dir_in_path():
-                            print(f"\n⚠ {_get_wrapper_dir()} is not in your PATH.")
+                            _wd = _get_wrapper_dir()
+                            print(f"\n⚠ {_wd} is not in your PATH.")
                             print(
                                 f"  Add to your shell config (~/.bashrc or ~/.zshrc):"
                             )
-                            print(f'    export PATH="$HOME/.local/bin:$PATH"')
+                            print(f'    export PATH="{_wd}:$PATH"')
 
             # Profile dir for display
             try:

hermes_cli/profiles.py

@@ -240,8 +240,25 @@ def _get_active_profile_path() -> Path:
 
 
 def _get_wrapper_dir() -> Path:
-    """Return the directory for wrapper scripts."""
-    return Path.home() / ".local" / "bin"
+    """Return the directory for profile-alias wrapper scripts.
+
+    Uses the canonical command-link directory so aliases land wherever the
+    ``hermes`` command itself lives and is therefore on PATH: ``/usr/local/bin``
+    for root FHS installs, ``$PREFIX/bin`` on Termux, ``~/.local/bin`` otherwise
+    (including Windows).  Previously hardcoded ``~/.local/bin``, which left
+    aliases off-PATH on root FHS installs (PR #38889).
+    """
+    from hermes_constants import command_link_dir
+
+    return command_link_dir()
+
+
+def _wrapper_candidate_dirs() -> list[Path]:
+    """All dirs a profile alias may live in, for cleanup that must find links
+    regardless of which layout created them."""
+    from hermes_constants import command_link_candidate_dirs
+
+    return command_link_candidate_dirs()
 
 
 # ---------------------------------------------------------------------------
@@ -399,27 +416,34 @@ def create_wrapper_script(name: str, target: Optional[str] = None) -> Optional[P
 
 
 def remove_wrapper_script(name: str) -> bool:
-    """Remove the wrapper script for a profile. Returns True if removed."""
-    wrapper_dir = _get_wrapper_dir()
+    """Remove the wrapper script for a profile. Returns True if removed.
+
+    Scans all candidate command-link directories (``~/.local/bin``,
+    ``/usr/local/bin``, ``$PREFIX/bin``) so aliases are removable regardless of
+    which layout created them — e.g. an alias written to ``/usr/local/bin`` on a
+    root FHS install, or a legacy one left in ``~/.local/bin``.
+    """
     canon = normalize_profile_name(name)
     is_windows = sys.platform == "win32"
 
-    # Check both the extensionless path (POSIX) and .bat (Windows)
-    candidates = [wrapper_dir / canon]
-    if is_windows:
-        candidates.insert(0, wrapper_dir / f"{canon}.bat")
+    removed = False
+    for wrapper_dir in _wrapper_candidate_dirs():
+        # Check both the extensionless path (POSIX) and .bat (Windows)
+        candidates = [wrapper_dir / canon]
+        if is_windows:
+            candidates.insert(0, wrapper_dir / f"{canon}.bat")
 
-    for wrapper_path in candidates:
-        if wrapper_path.exists():
-            try:
-                # Verify it's our wrapper before removing
-                content = wrapper_path.read_text()
-                if "hermes -p" in content:
-                    wrapper_path.unlink()
-                    return True
-            except Exception:
-                pass
-    return False
+        for wrapper_path in candidates:
+            if wrapper_path.exists():
+                try:
+                    # Verify it's our wrapper before removing
+                    content = wrapper_path.read_text()
+                    if "hermes -p" in content:
+                        wrapper_path.unlink()
+                        removed = True
+                except Exception:
+                    pass
+    return removed
 
 
 # ---------------------------------------------------------------------------

hermes_cli/uninstall.py

@@ -9,6 +9,7 @@ Provides options for:
 import os
 import shutil
 import subprocess
+import sys
 from pathlib import Path
 
 from hermes_constants import get_hermes_home
@@ -117,45 +118,58 @@ def remove_wrapper_script():
     return removed
 
 
+def _node_symlink_candidate_dirs() -> "list[Path]":
+    """Directories where the installer may have placed node/npm/npx symlinks.
+
+    Delegates to the canonical helper in hermes_constants so the layout logic
+    lives in exactly one place (shared with profiles, doctor, backup).
+    """
+    from hermes_constants import command_link_candidate_dirs
+
+    return command_link_candidate_dirs()
+
+
 def remove_node_symlinks(hermes_home: Path) -> list:
-    """Remove the node/npm/npx symlinks the installer drops in ~/.local/bin.
+    """Remove the node/npm/npx symlinks the installer placed on PATH.
 
     The POSIX installer (``scripts/install.sh`` / ``scripts/lib/node-bootstrap.sh``)
-    creates::
+    symlinks node/npm/npx into the same directory as the ``hermes`` command:
 
-        ~/.local/bin/node -> $HERMES_HOME/node/bin/node
-        ~/.local/bin/npm  -> $HERMES_HOME/node/bin/npm
-        ~/.local/bin/npx  -> $HERMES_HOME/node/bin/npx
+    - ``/usr/local/bin/`` on root FHS installs (Linux, uid 0)
+    - ``$PREFIX/bin/`` on Termux
+    - ``~/.local/bin/`` otherwise (the common non-root case)
 
-    and prepends ``~/.local/bin`` to PATH, so these shadow an existing Node
-    manager such as nvm.  Symmetrically remove them on uninstall, but *only*
-    when the link still resolves into this Hermes home's ``node`` directory.
-    A link the user has since repointed at nvm (or anything else outside
-    Hermes) is left untouched so we never break unrelated tooling.
+    We check all candidate directories so that uninstall works regardless of
+    how the install was done (e.g. a root FHS install that placed links in
+    ``/usr/local/bin``, or an older install that used ``~/.local/bin`` before
+    the FHS fix).  Only symlinks that resolve into this Hermes home's ``node``
+    directory are removed — links the user has repointed elsewhere (nvm, fnm,
+    etc.) are left untouched.
     """
     node_dir = (hermes_home / "node").resolve()
     removed = []
 
     for name in ("node", "npm", "npx"):
-        link = Path.home() / ".local" / "bin" / name
-        try:
-            # Only act on symlinks — never delete a real binary the user put here.
-            if not link.is_symlink():
-                continue
+        for bin_dir in _node_symlink_candidate_dirs():
+            link = bin_dir / name
+            try:
+                # Only act on symlinks — never delete a real binary the user put here.
+                if not link.is_symlink():
+                    continue
 
-            # Resolve the link target and confirm it points into our node dir.
-            # os.readlink + manual join handles broken (dangling) links too;
-            # Path.resolve() on a dangling link still returns the target path.
-            target = Path(os.readlink(link))
-            if not target.is_absolute():
-                target = (link.parent / target)
-            target = target.resolve()
+                # Resolve the link target and confirm it points into our node dir.
+                # os.readlink + manual join handles broken (dangling) links too;
+                # Path.resolve() on a dangling link still returns the target path.
+                target = Path(os.readlink(link))
+                if not target.is_absolute():
+                    target = (link.parent / target)
+                target = target.resolve()
 
-            if target == node_dir or node_dir in target.parents:
-                link.unlink()
-                removed.append(link)
-        except Exception as e:
-            log_warn(f"Could not remove {link}: {e}")
+                if target == node_dir or node_dir in target.parents:
+                    link.unlink()
+                    removed.append(link)
+            except Exception as e:
+                log_warn(f"Could not remove {link}: {e}")
 
     return removed
 
@@ -458,14 +472,28 @@ def _uninstall_profile(profile) -> None:
         except Exception as e:
             log_warn(f"  Could not run gateway {subcmd} for '{name}': {e}")
 
-    # 2. Remove the wrapper alias script at ~/.local/bin/<name> (if any).
-    alias_path = getattr(profile, "alias_path", None)
-    if alias_path and alias_path.exists():
-        try:
-            alias_path.unlink()
-            log_success(f"  Removed alias {alias_path}")
-        except Exception as e:
-            log_warn(f"  Could not remove alias {alias_path}: {e}")
+    # 2. Remove the wrapper alias script wherever it landed.  Use the
+    #    profiles helper which scans all candidate command-link dirs
+    #    (~/.local/bin, /usr/local/bin, $PREFIX/bin) so root FHS aliases are
+    #    removed too — then fall back to the recorded alias_path for safety.
+    removed_alias = False
+    try:
+        from hermes_cli.profiles import remove_wrapper_script
+
+        removed_alias = remove_wrapper_script(name)
+        if removed_alias:
+            log_success(f"  Removed profile alias '{name}'")
+    except Exception as e:
+        log_warn(f"  Could not scan for profile alias '{name}': {e}")
+
+    if not removed_alias:
+        alias_path = getattr(profile, "alias_path", None)
+        if alias_path and alias_path.exists():
+            try:
+                alias_path.unlink()
+                log_success(f"  Removed alias {alias_path}")
+            except Exception as e:
+                log_warn(f"  Could not remove alias {alias_path}: {e}")
 
     # 3. Wipe the profile's HERMES_HOME directory.
     try:

hermes_constants.py

@@ -414,6 +414,145 @@ def get_env_path() -> Path:
     return get_hermes_home() / ".env"
 
 
+# ─── Command-Link & Bundled-Node Locations ───────────────────────────────────
+#
+# Canonical, single source of truth for *where the installer places executables
+# so they land on PATH*.  This MUST stay in lockstep with the bash helper
+# ``get_command_link_dir()`` in ``scripts/install.sh`` and ``_nb_get_link_dir()``
+# in ``scripts/lib/node-bootstrap.sh``.  Historically this logic was duplicated
+# (and went stale) in doctor.py, profiles.py, uninstall.py and backup.py, which
+# caused root-FHS installs to look for / write the ``hermes`` command and node
+# symlinks in ``~/.local/bin`` even though they actually live in
+# ``/usr/local/bin``.  See PR #38889.
+
+
+def _is_root_fhs_layout() -> bool:
+    """Return True when this is a root install using the Linux FHS layout.
+
+    Mirrors ``resolve_install_layout()`` in ``scripts/install.sh``: root (uid 0)
+    on Linux uses ``/usr/local/lib/hermes-agent`` for code and ``/usr/local/bin``
+    for the command link.  We detect it the same way the installer's own runtime
+    guard does (``_ensure_fhs_path_guard`` in main.py): Linux + uid 0 + a command
+    link present at ``/usr/local/bin/hermes`` OR code at
+    ``/usr/local/lib/hermes-agent``.  Falling back to the uid check alone keeps
+    this correct *during* an install before the symlink exists.
+    """
+    if sys.platform != "linux":
+        return False
+    try:
+        if not hasattr(os, "geteuid") or os.geteuid() != 0:
+            return False
+    except OSError:
+        return False
+    # Confirm it's actually the FHS layout (not a root user who installed into
+    # ~/.local/bin anyway).  A legacy git install at <HERMES_HOME>/hermes-agent
+    # means resolve_install_layout() kept the ~/.local/bin layout — mirror that.
+    if (get_hermes_home() / "hermes-agent" / ".git").exists():
+        return False
+    if Path("/usr/local/bin/hermes").exists():
+        return True
+    if Path("/usr/local/lib/hermes-agent").exists():
+        return True
+    # No markers yet (e.g. mid-install): for a Linux root user the installer
+    # defaults to the FHS layout, so assume FHS.
+    return True
+
+
+def command_link_dir() -> Path:
+    """Return the directory where the ``hermes`` command (and bundled node/npm/
+    npx symlinks, profile-alias wrappers) are placed so they land on PATH.
+
+    Resolution mirrors ``get_command_link_dir()`` in ``scripts/install.sh``:
+
+    * Termux  → ``$PREFIX/bin``
+    * root FHS install on Linux → ``/usr/local/bin``
+    * everything else (the common non-root case, and Windows) → ``~/.local/bin``
+    """
+    if is_termux():
+        prefix = os.environ.get("PREFIX", "").strip()
+        if prefix:
+            return Path(prefix) / "bin"
+    if _is_root_fhs_layout():
+        return Path("/usr/local/bin")
+    return Path.home() / ".local" / "bin"
+
+
+def command_link_display_dir() -> str:
+    """User-friendly display string for :func:`command_link_dir`.
+
+    Uses ``~/.local/bin`` shorthand and ``$PREFIX/bin`` for Termux, matching
+    ``get_command_link_display_dir()`` in ``scripts/install.sh``.
+    """
+    if is_termux() and os.environ.get("PREFIX", "").strip():
+        return "$PREFIX/bin"
+    if _is_root_fhs_layout():
+        return "/usr/local/bin"
+    return "~/.local/bin"
+
+
+def command_link_candidate_dirs() -> list[Path]:
+    """All directories the installer may have placed command links in.
+
+    Used by uninstall and other cleanup paths that must find links regardless
+    of which layout created them (e.g. an old ``~/.local/bin`` install upgraded
+    to FHS, or vice-versa).  Always includes ``~/.local/bin`` plus the
+    layout-specific dirs, de-duplicated and order-preserving.
+    """
+    dirs: list[Path] = [Path.home() / ".local" / "bin"]
+    if sys.platform == "linux":
+        dirs.append(Path("/usr/local/bin"))
+    prefix = os.environ.get("PREFIX", "").strip()
+    if prefix and "com.termux" in prefix:
+        dirs.append(Path(prefix) / "bin")
+    # De-dupe while preserving order.
+    seen: set[str] = set()
+    out: list[Path] = []
+    for d in dirs:
+        key = str(d)
+        if key not in seen:
+            seen.add(key)
+            out.append(d)
+    return out
+
+
+def bundled_node_bin_dir() -> Path:
+    """Return the bundled Node.js ``bin`` directory: ``<HERMES_HOME>/node/bin``.
+
+    This is where ``install_node()`` / ``node-bootstrap.sh`` extract the
+    Hermes-managed Node runtime.  Profile-aware via :func:`get_hermes_home`.
+    Discovery code that gates a feature on ``node``/``npm``/``npx`` should fall
+    back to this directory when ``shutil.which`` returns nothing, so a misplaced
+    or missing PATH symlink doesn't make an installed runtime invisible.
+    """
+    return get_hermes_home() / "node" / "bin"
+
+
+def find_node_executable(name: str = "node") -> str | None:
+    """Resolve a Node executable (node/npm/npx) with bundled fallback.
+
+    Returns an absolute path string if found on PATH or in the bundled
+    ``<HERMES_HOME>/node/bin`` directory, else ``None``.  Prefer this over a
+    bare ``shutil.which(name)`` anywhere a feature depends on Node, so an
+    off-PATH bundled install still works.
+    """
+    import shutil
+
+    on_path = shutil.which(name)
+    if on_path:
+        return on_path
+    candidate = bundled_node_bin_dir() / name
+    if sys.platform == "win32" and not candidate.suffix:
+        # Windows ships node.exe / npm.cmd; try common suffixes.
+        for suffix in (".exe", ".cmd", ".bat", ""):
+            c = candidate.with_suffix(suffix) if suffix else candidate
+            if c.exists() and os.access(c, os.X_OK):
+                return str(c)
+        return None
+    if candidate.exists() and os.access(candidate, os.X_OK):
+        return str(candidate)
+    return None
+
+
 # ─── Network Preferences ─────────────────────────────────────────────────────
 
 

scripts/install.sh

@@ -731,6 +731,12 @@ check_node() {
     # Prefer a Hermes-managed Node from a previous run over a too-old system one.
     if [ -x "$HERMES_HOME/node/bin/node" ] && node_satisfies_build "$("$HERMES_HOME/node/bin/node" --version)"; then
         export PATH="$HERMES_HOME/node/bin:$PATH"
+        # Migration repair (#38889): a previously-broken install may have its
+        # node symlinks only in ~/.local/bin (off-PATH on root FHS) or missing.
+        # Re-link into the canonical dir + prune stale copies so re-running the
+        # installer (or `hermes update`) heals the box instead of leaving it
+        # broken.
+        link_bundled_node
         log_success "Node.js $("$HERMES_HOME/node/bin/node" --version) found (Hermes-managed)"
         HAS_NODE=true
         return 0
@@ -746,6 +752,31 @@ check_node() {
     install_node
 }
 
+# Idempotently (re)create node/npm/npx PATH symlinks in the command-link dir
+# and prune stale ones in the other candidate dirs.  Shared by install_node
+# (fresh install) and check_node (migration repair of an existing broken box,
+# #38889).  Pruning only removes symlinks that resolve into THIS Hermes home's
+# node dir — never a real binary or a user's nvm/fnm link.
+link_bundled_node() {
+    local node_link_dir stale_dir name target
+    node_link_dir="$(get_command_link_dir)"
+    mkdir -p "$node_link_dir"
+    ln -sf "$HERMES_HOME/node/bin/node" "$node_link_dir/node"
+    ln -sf "$HERMES_HOME/node/bin/npm"  "$node_link_dir/npm"
+    ln -sf "$HERMES_HOME/node/bin/npx"  "$node_link_dir/npx"
+
+    for stale_dir in "$HOME/.local/bin" "/usr/local/bin"; do
+        [ "$stale_dir" = "$node_link_dir" ] && continue
+        for name in node npm npx; do
+            [ -L "$stale_dir/$name" ] || continue
+            target="$(readlink "$stale_dir/$name" 2>/dev/null || true)"
+            case "$target" in
+                "$HERMES_HOME/node/"*) rm -f "$stale_dir/$name" ;;
+            esac
+        done
+    done
+}
+
 install_node() {
     if [ "$DISTRO" = "termux" ]; then
         log_info "Installing Node.js via pkg..."
@@ -836,16 +867,15 @@ install_node() {
         return 0
     fi
 
-    # Place into ~/.hermes/node/ and symlink binaries to ~/.local/bin/
+    # Place into ~/.hermes/node/ and symlink binaries into the same bin dir
+    # the hermes command uses (get_command_link_dir): /usr/local/bin for root
+    # FHS installs, $PREFIX/bin on Termux, ~/.local/bin otherwise.
     rm -rf "$HERMES_HOME/node"
     mkdir -p "$HERMES_HOME"
     mv "$extracted_dir" "$HERMES_HOME/node"
     rm -rf "$tmp_dir"
 
-    mkdir -p "$HOME/.local/bin"
-    ln -sf "$HERMES_HOME/node/bin/node" "$HOME/.local/bin/node"
-    ln -sf "$HERMES_HOME/node/bin/npm"  "$HOME/.local/bin/npm"
-    ln -sf "$HERMES_HOME/node/bin/npx"  "$HOME/.local/bin/npx"
+    link_bundled_node
 
     export PATH="$HERMES_HOME/node/bin:$PATH"
 

scripts/lib/node-bootstrap.sh

@@ -44,6 +44,63 @@ _nb_is_termux() {
     [ -n "${TERMUX_VERSION:-}" ] || [[ "${PREFIX:-}" == *"com.termux/files/usr"* ]]
 }
 
+# Where to symlink node/npm/npx so they land on PATH.
+# Mirrors get_command_link_dir() from install.sh: root FHS → /usr/local/bin,
+# Termux → $PREFIX/bin, otherwise ~/.local/bin.
+#
+# Parity note (#38889): install.sh keys off $ROOT_FHS_LAYOUT, which
+# resolve_install_layout() sets to FALSE for a root user who has a LEGACY
+# install at $HERMES_HOME/hermes-agent/.git (those keep ~/.local/bin).  We
+# mirror that here so the bootstrap path (hermes update) can't diverge from the
+# installer and link node into a different dir than the hermes command.
+_nb_get_link_dir() {
+    if _nb_is_termux && [ -n "${PREFIX:-}" ]; then
+        echo "$PREFIX/bin"
+        return
+    fi
+    if [ "$(id -u)" = 0 ] && [ "$(uname -s)" = "Linux" ]; then
+        # Root on Linux: FHS layout UNLESS a legacy git install exists, matching
+        # resolve_install_layout() in install.sh.
+        if [ -d "${HERMES_HOME:-$HOME/.hermes}/hermes-agent/.git" ]; then
+            echo "$HOME/.local/bin"
+        else
+            echo "/usr/local/bin"
+        fi
+        return
+    fi
+    echo "$HOME/.local/bin"
+}
+
+# Idempotently (re)create the node/npm/npx PATH symlinks in the canonical link
+# dir, and prune stale ones left in OTHER candidate dirs by an older/broken
+# install (the #38889 migration case: a root box upgraded from the old layout
+# has links only in ~/.local/bin, off-PATH).  Safe to call repeatedly.
+#
+# Pruning rule mirrors hermes_cli/uninstall.remove_node_symlinks: only remove a
+# symlink that still resolves into THIS Hermes home's node dir — never touch a
+# real binary or a link the user repointed at nvm/fnm.
+_nb_link_bundled_node() {
+    local link_dir stale_dir name target
+    link_dir="$(_nb_get_link_dir)"
+    mkdir -p "$link_dir"
+    ln -sf "$HERMES_HOME/node/bin/node" "$link_dir/node"
+    ln -sf "$HERMES_HOME/node/bin/npm"  "$link_dir/npm"
+    ln -sf "$HERMES_HOME/node/bin/npx"  "$link_dir/npx"
+
+    # Prune stale links in the other candidate dirs (so a migrated root install
+    # doesn't keep shadowing copies in ~/.local/bin — #34536 nvm-shadow class).
+    for stale_dir in "$HOME/.local/bin" "/usr/local/bin"; do
+        [ "$stale_dir" = "$link_dir" ] && continue
+        for name in node npm npx; do
+            [ -L "$stale_dir/$name" ] || continue
+            target="$(readlink "$stale_dir/$name" 2>/dev/null || true)"
+            case "$target" in
+                "$HERMES_HOME/node/"*) rm -f "$stale_dir/$name" ;;
+            esac
+        done
+    done
+}
+
 _nb_node_major() {
     local v
     v=$(node --version 2>/dev/null | sed 's/^v//' | cut -d. -f1)
@@ -187,10 +244,8 @@ _nb_install_bundled_node() {
     mv "$extracted" "$HERMES_HOME/node"
     rm -rf "$tmp"
 
-    mkdir -p "$HOME/.local/bin"
-    ln -sf "$HERMES_HOME/node/bin/node" "$HOME/.local/bin/node"
-    ln -sf "$HERMES_HOME/node/bin/npm"  "$HOME/.local/bin/npm"
-    ln -sf "$HERMES_HOME/node/bin/npx"  "$HOME/.local/bin/npx"
+    # Create PATH symlinks in the canonical link dir (and prune stale ones).
+    _nb_link_bundled_node
     export PATH="$HERMES_HOME/node/bin:$PATH"
 
     _nb_have_modern_node || return 1
@@ -214,6 +269,12 @@ ensure_node() {
     if [ -x "$HERMES_HOME/node/bin/node" ]; then
         export PATH="$HERMES_HOME/node/bin:$PATH"
         if _nb_have_modern_node; then
+            # Migration repair (#38889): an existing install may have its node
+            # symlinks only in ~/.local/bin (off-PATH on root FHS) or missing
+            # entirely.  Re-create them in the canonical link dir and prune
+            # stale copies, so `hermes update` heals a previously-broken box
+            # instead of silently leaving it broken.
+            _nb_link_bundled_node
             _nb_ok "Node $(node --version) found (Hermes-managed)"
             HERMES_NODE_AVAILABLE=true
             return 0

tests/hermes_cli/test_profiles.py

@@ -1288,3 +1288,48 @@ class TestEdgeCases:
             delete_profile("coder", yes=True)
 
         assert get_active_profile() == "default"
+
+
+class TestWrapperDirLayoutAware:
+    """Profile-alias wrapper dir follows the canonical command-link layout (#38889)."""
+
+    def test_wrapper_dir_root_fhs(self, monkeypatch):
+        import hermes_cli.profiles as profiles
+        import hermes_constants
+        monkeypatch.setattr(hermes_constants, "is_termux", lambda: False)
+        monkeypatch.setattr(hermes_constants, "_is_root_fhs_layout", lambda: True)
+        assert profiles._get_wrapper_dir() == Path("/usr/local/bin")
+
+    def test_wrapper_dir_nonroot(self, tmp_path, monkeypatch):
+        import hermes_cli.profiles as profiles
+        import hermes_constants
+        monkeypatch.setattr(Path, "home", lambda: tmp_path)
+        monkeypatch.setattr(hermes_constants, "is_termux", lambda: False)
+        monkeypatch.setattr(hermes_constants, "_is_root_fhs_layout", lambda: False)
+        assert profiles._get_wrapper_dir() == tmp_path / ".local" / "bin"
+
+    def test_remove_wrapper_scans_all_dirs(self, tmp_path, monkeypatch):
+        """An alias in /usr/local/bin is removed even though _get_wrapper_dir
+        would (in test) point at ~/.local/bin — remove must scan candidates."""
+        import hermes_cli.profiles as profiles
+        fake_usr_local = tmp_path / "usr_local_bin"
+        fake_usr_local.mkdir()
+        alias = fake_usr_local / "myprof"
+        alias.write_text('#!/usr/bin/env bash\nexec hermes -p myprof "$@"\n')
+        alias.chmod(0o755)
+        monkeypatch.setattr(
+            profiles, "_wrapper_candidate_dirs", lambda: [fake_usr_local]
+        )
+        assert profiles.remove_wrapper_script("myprof") is True
+        assert not alias.exists()
+
+    def test_remove_wrapper_leaves_foreign_files(self, tmp_path, monkeypatch):
+        """A file that isn't our wrapper (no 'hermes -p') is left untouched."""
+        import hermes_cli.profiles as profiles
+        d = tmp_path / "bin"
+        d.mkdir()
+        foreign = d / "myprof"
+        foreign.write_text("#!/bin/sh\necho not ours\n")
+        monkeypatch.setattr(profiles, "_wrapper_candidate_dirs", lambda: [d])
+        assert profiles.remove_wrapper_script("myprof") is False
+        assert foreign.exists()

tests/hermes_cli/test_uninstall_node_symlinks.py

@@ -130,3 +130,37 @@ def test_only_some_links_present(fake_home):
     assert (local_bin / "node").exists()
     assert not (local_bin / "npm").is_symlink()
     assert not (local_bin / "npx").is_symlink()
+
+
+def test_removes_fhs_symlinks_in_usr_local_bin(fake_home, tmp_path, monkeypatch):
+    """Root FHS installs place node symlinks in /usr/local/bin.
+
+    We monkeypatch _node_symlink_candidate_dirs to return a temp dir standing
+    in for /usr/local/bin so the test doesn't need real root privileges.
+    """
+    hermes_home = fake_home / ".hermes"
+    node_bin = _make_hermes_node(hermes_home)
+
+    # Fake /usr/local/bin as a temp dir with our symlinks.
+    fhs_bin = tmp_path / "usr_local_bin"
+    fhs_bin.mkdir()
+    for name in ("node", "npm", "npx"):
+        (fhs_bin / name).symlink_to(node_bin / name)
+
+    # Ensure ~/.local/bin has NO symlinks (simulate pure FHS install).
+    local_bin = fake_home / ".local" / "bin"
+    for name in ("node", "npm", "npx"):
+        p = local_bin / name
+        if p.exists() or p.is_symlink():
+            p.unlink()
+
+    # Return only our fake FHS dir as a candidate.
+    monkeypatch.setattr(
+        uninstall, "_node_symlink_candidate_dirs", lambda: [fhs_bin]
+    )
+
+    removed = uninstall.remove_node_symlinks(hermes_home)
+
+    assert sorted(p.name for p in removed) == ["node", "npm", "npx"]
+    for name in ("node", "npm", "npx"):
+        assert not (fhs_bin / name).is_symlink()

tests/test_hermes_constants.py

@@ -298,3 +298,66 @@ class TestSecureParentDir:
         assert len(called_with) == 1
         assert called_with[0] == (str(real_dir), 0o700)
 
+
+
+class TestCommandLinkDir:
+    """Tests for the canonical command-link / bundled-node helpers (#38889)."""
+
+    def test_nonroot_returns_local_bin(self, tmp_path, monkeypatch):
+        monkeypatch.setattr(Path, "home", lambda: tmp_path)
+        monkeypatch.delenv("PREFIX", raising=False)
+        monkeypatch.setattr(hermes_constants, "is_termux", lambda: False)
+        monkeypatch.setattr(hermes_constants, "_is_root_fhs_layout", lambda: False)
+        assert hermes_constants.command_link_dir() == tmp_path / ".local" / "bin"
+        assert hermes_constants.command_link_display_dir() == "~/.local/bin"
+
+    def test_root_fhs_returns_usr_local_bin(self, monkeypatch):
+        monkeypatch.setattr(hermes_constants, "is_termux", lambda: False)
+        monkeypatch.setattr(hermes_constants, "_is_root_fhs_layout", lambda: True)
+        assert hermes_constants.command_link_dir() == Path("/usr/local/bin")
+        assert hermes_constants.command_link_display_dir() == "/usr/local/bin"
+
+    def test_termux_returns_prefix_bin(self, monkeypatch):
+        monkeypatch.setattr(hermes_constants, "is_termux", lambda: True)
+        monkeypatch.setenv("PREFIX", "/data/data/com.termux/files/usr")
+        assert hermes_constants.command_link_dir() == Path(
+            "/data/data/com.termux/files/usr/bin"
+        )
+        assert hermes_constants.command_link_display_dir() == "$PREFIX/bin"
+
+    def test_candidate_dirs_includes_both_on_linux(self, tmp_path, monkeypatch):
+        monkeypatch.setattr(Path, "home", lambda: tmp_path)
+        monkeypatch.setattr(hermes_constants.sys, "platform", "linux")
+        monkeypatch.delenv("PREFIX", raising=False)
+        dirs = hermes_constants.command_link_candidate_dirs()
+        assert tmp_path / ".local" / "bin" in dirs
+        assert Path("/usr/local/bin") in dirs
+
+    def test_candidate_dirs_deduped(self, tmp_path, monkeypatch):
+        monkeypatch.setattr(Path, "home", lambda: tmp_path)
+        monkeypatch.setattr(hermes_constants.sys, "platform", "linux")
+        monkeypatch.delenv("PREFIX", raising=False)
+        dirs = hermes_constants.command_link_candidate_dirs()
+        assert len(dirs) == len({str(d) for d in dirs})
+
+    def test_bundled_node_bin_dir(self, tmp_path, monkeypatch):
+        monkeypatch.setenv("HERMES_HOME", str(tmp_path))
+        assert hermes_constants.bundled_node_bin_dir() == tmp_path / "node" / "bin"
+
+    def test_find_node_prefers_path(self, monkeypatch):
+        monkeypatch.setattr("shutil.which", lambda n: "/usr/bin/" + n)
+        assert hermes_constants.find_node_executable("node") == "/usr/bin/node"
+
+    def test_find_node_falls_back_to_bundled(self, tmp_path, monkeypatch):
+        monkeypatch.setenv("HERMES_HOME", str(tmp_path))
+        monkeypatch.setattr("shutil.which", lambda n: None)
+        node_bin = tmp_path / "node" / "bin"
+        node_bin.mkdir(parents=True)
+        (node_bin / "npm").write_text("#!/bin/sh\n")
+        (node_bin / "npm").chmod(0o755)
+        assert hermes_constants.find_node_executable("npm") == str(node_bin / "npm")
+
+    def test_find_node_returns_none_when_absent(self, tmp_path, monkeypatch):
+        monkeypatch.setenv("HERMES_HOME", str(tmp_path))
+        monkeypatch.setattr("shutil.which", lambda n: None)
+        assert hermes_constants.find_node_executable("node") is None