feat(skills): add llm-wiki skill for persistent markdown knowledge bases

Based on Andrej Karpathy's LLM Wiki pattern. Teaches the agent to build and
maintain interlinked markdown wikis that compound knowledge over time — an
alternative to traditional RAG.

Three core operations:
- Ingest: capture raw sources, write summaries, update entity/concept pages,
  cross-reference across the wiki
- Query: synthesize answers from compiled knowledge, file valuable results
  back into the wiki
- Lint: find contradictions, orphan pages, stale content, data gaps

Includes three-layer architecture (raw sources / wiki pages / schema),
index.md + log.md navigation pattern, YAML frontmatter conventions,
and Obsidian integration guidance.

skills/research/llm-wiki/SKILL.md

@@ -0,0 +1,274 @@
+---
+name: llm-wiki
+description: "Karpathy's LLM Wiki — build and maintain a persistent, interlinked markdown knowledge base. Ingest sources, query compiled knowledge, and lint for consistency."
+version: 1.0.0
+author: Hermes Agent
+license: MIT
+metadata:
+  hermes:
+    tags: [wiki, knowledge-base, research, notes, markdown, rag-alternative]
+    category: research
+    related_skills: [obsidian, arxiv, agentic-research-ideas]
+---
+
+# Karpathy's LLM Wiki
+
+Build and maintain a persistent, compounding knowledge base as interlinked markdown files.
+Based on [Andrej Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f).
+
+Unlike traditional RAG (which rediscovers knowledge from scratch per query), the wiki
+compiles knowledge once and keeps it current. Cross-references are already there.
+Contradictions have already been flagged. Synthesis reflects everything ingested.
+
+**Division of labor:** The human curates sources and directs analysis. The agent
+summarizes, cross-references, files, and maintains consistency.
+
+## Wiki Location
+
+Set `LLM_WIKI_PATH` in `~/.hermes/.env` to choose where the wiki lives.
+
+Default: `~/wiki`
+
+The wiki is just a directory of markdown files — open it in Obsidian, VS Code, or
+any editor. No database, no special tooling required.
+
+## Architecture: Three Layers
+
+```
+wiki/
+├── SCHEMA.md           # Conventions, structure rules, domain config
+├── index.md            # Content catalog — every page with one-line summary
+├── log.md              # Chronological action log (append-only)
+├── raw/                # Layer 1: Immutable source material
+│   ├── articles/       # Web articles, clippings
+│   ├── papers/         # PDFs, arxiv papers
+│   ├── transcripts/    # Meeting notes, interviews
+│   └── assets/         # Images, diagrams referenced by sources
+├── entities/           # Layer 2: Entity pages (people, orgs, products)
+├── concepts/           # Layer 2: Concept/topic pages
+├── comparisons/        # Layer 2: Side-by-side analyses
+└── queries/            # Layer 2: Filed query results worth keeping
+```
+
+**Layer 1 — Raw Sources:** Immutable. The agent reads but never modifies these.
+**Layer 2 — The Wiki:** Agent-owned markdown files. Created, updated, and
+cross-referenced by the agent.
+**Layer 3 — The Schema:** `SCHEMA.md` defines structure and conventions.
+
+## Initializing a Wiki
+
+When the user asks to create or start a wiki:
+
+1. Determine the wiki path (from `LLM_WIKI_PATH` env var, or ask the user, or default to `~/wiki`)
+2. Create the directory structure above
+3. Write `SCHEMA.md` customized to the user's domain (ask what the wiki is about)
+4. Write initial `index.md` with header and empty catalog
+5. Write initial `log.md` with creation entry
+6. Confirm the wiki is ready
+
+```bash
+# Check/create wiki path
+WIKI="${LLM_WIKI_PATH:-$HOME/wiki}"
+```
+
+### SCHEMA.md Template
+
+Adapt this to the user's domain. The schema prevents generic chatbot behavior
+and makes the agent a disciplined maintainer:
+
+```markdown
+# Wiki Schema
+
+## Domain
+[What this wiki covers — e.g., "AI/ML research", "personal health", "startup intelligence"]
+
+## Conventions
+- File names: lowercase, hyphens, no spaces (e.g., `transformer-architecture.md`)
+- Every wiki page starts with a YAML frontmatter block:
+  ```yaml
+  ---
+  title: Page Title
+  created: YYYY-MM-DD
+  updated: YYYY-MM-DD
+  type: entity | concept | comparison | query | summary
+  tags: [tag1, tag2]
+  sources: [raw/articles/source-name.md]
+  ---
+  ```
+- Use `[[wikilinks]]` to link between pages
+- When updating a page, always bump the `updated` date
+- Every new page must be added to `index.md`
+- Every action must be appended to `log.md`
+
+## Entity Pages
+One page per notable entity (person, company, model, tool). Include:
+- Overview / what it is
+- Key facts and dates
+- Relationships to other entities
+- Source references
+
+## Concept Pages
+One page per concept or topic. Include:
+- Definition / explanation
+- Current state of knowledge
+- Open questions or debates
+- Related concepts (wikilinks)
+
+## Comparison Pages
+Side-by-side analyses. Include:
+- What is being compared and why
+- Dimensions of comparison (table format preferred)
+- Verdict or synthesis
+- Sources
+
+## Source Summaries
+When ingesting a raw source, write a summary in the source's directory:
+`raw/articles/source-name.md` (the original) gets a companion summary that
+lives as a wiki page.
+```
+
+### index.md Template
+
+```markdown
+# Wiki Index
+
+> Content catalog. Every wiki page with a one-line summary.
+> Read this first to find relevant files for any query.
+
+## Entities
+<!-- entity pages listed here -->
+
+## Concepts
+<!-- concept pages listed here -->
+
+## Comparisons
+<!-- comparison pages listed here -->
+
+## Queries
+<!-- filed query results listed here -->
+```
+
+### log.md Template
+
+```markdown
+# Wiki Log
+
+> Chronological record of all wiki actions. Append-only.
+> Format: `## [YYYY-MM-DD] action | subject`
+> Actions: ingest, update, query, lint, create, delete
+
+## [YYYY-MM-DD] create | Wiki initialized
+- Domain: [domain]
+- Structure created with SCHEMA.md, index.md, log.md
+```
+
+## Core Operations
+
+### 1. Ingest
+
+When the user provides a source (URL, file, paste), integrate it into the wiki:
+
+① **Capture the raw source:**
+   - URL → use `web_extract` to get markdown, save to `raw/articles/`
+   - PDF → use `web_extract` (handles PDFs), save to `raw/papers/`
+   - Pasted text → save to appropriate `raw/` subdirectory
+   - Name the file descriptively: `raw/articles/karpathy-llm-wiki-2026.md`
+
+② **Discuss takeaways** with the user — what's interesting, what matters for the domain.
+
+③ **Write or update wiki pages:**
+   - Create a summary page if the source is substantial
+   - Create or update entity pages for key people/orgs/tools mentioned
+   - Create or update concept pages for key ideas
+   - Add cross-references (`[[wikilinks]]`) between new and existing pages
+
+④ **Update navigation:**
+   - Add new pages to `index.md` with one-line summaries
+   - Append to `log.md`: `## [YYYY-MM-DD] ingest | Source Title`
+
+⑤ **Report what changed** — list every file created or updated.
+
+A single source can trigger updates across 10-15 wiki pages. This is normal
+and desired — it's the compounding effect.
+
+### 2. Query
+
+When the user asks a question:
+
+① **Read `index.md`** to identify relevant pages.
+② **Read the relevant pages** using `read_file`.
+③ **Synthesize an answer** from the compiled knowledge.
+④ **File valuable answers back** — if the answer is a substantial comparison,
+   deep dive, or discovery, create a new page in `queries/` or `comparisons/`
+   so it doesn't disappear into chat history.
+⑤ **Update log.md** with the query.
+
+For large wikis (100+ pages), use `search_files` to search content across all
+markdown files before synthesizing.
+
+### 3. Lint
+
+When the user asks to lint, health-check, or audit the wiki:
+
+① **Scan for contradictions:** Read pages on the same topic and flag conflicting claims.
+② **Find orphan pages:** Pages with no inbound `[[wikilinks]]` from other pages.
+③ **Check for stale content:** Pages whose `updated` date is old relative to newer sources.
+④ **Identify data gaps:** Topics referenced but lacking dedicated pages.
+⑤ **Verify index completeness:** Every wiki page should appear in `index.md`.
+⑥ **Report findings** with specific file paths and suggested actions.
+⑦ **Append to log.md:** `## [YYYY-MM-DD] lint | N issues found`
+
+Lint command for finding orphan pages:
+
+```python
+# Find all wiki pages
+# For each, check if any OTHER page links to it via [[filename]]
+# Pages with zero inbound links are orphans
+```
+
+## Working with the Wiki
+
+### Searching
+
+```bash
+# Find pages by content
+search_files "transformer" path="$WIKI" file_glob="*.md"
+
+# Find pages by filename
+search_files "*.md" target="files" path="$WIKI"
+
+# Recent log activity
+grep "^## \[" "$WIKI/log.md" | tail -10
+```
+
+### Bulk Operations
+
+When ingesting multiple sources at once, batch the updates:
+- Read all sources first
+- Identify all entities and concepts across sources
+- Create/update pages in one pass (avoids redundant updates)
+- Update index.md once at the end
+- Write a single log entry covering the batch
+
+### Obsidian Integration
+
+If the user has Obsidian, the wiki directory works as a vault out of the box:
+- `[[wikilinks]]` render as clickable links
+- Graph View visualizes the knowledge network
+- YAML frontmatter powers Dataview queries
+- The `raw/assets/` folder holds images referenced via `![[image.png]]`
+
+Set `OBSIDIAN_VAULT_PATH` to the same directory as `LLM_WIKI_PATH` to use
+both the Obsidian skill and this skill on the same vault.
+
+## Pitfalls
+
+- **Never modify files in `raw/`** — sources are immutable. Corrections go in wiki pages.
+- **Always update index.md and log.md** — skipping this makes the wiki degrade over time.
+- **Don't create pages without cross-references** — isolated pages are invisible. Every
+  page should link to at least one other page.
+- **Frontmatter is required** — it enables search, filtering, and staleness detection.
+- **Keep summaries concise** — a wiki page should be scannable in 30 seconds. Move
+  detailed analysis to dedicated deep-dive pages.
+- **Ask before mass-updating** — if an ingest would touch 10+ existing pages, confirm
+  the scope with the user first.