Add AGENTS.md + GEMINI.md for Codex, OpenCode, Gemini CLI support

The wiki now works with any coding agent that reads a repo config file. CLAUDE.md → Claude Code, AGENTS.md → Codex/OpenCode, GEMINI.md → Gemini CLI. README updated with agent compatibility table. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2026-04-07 07:09:13 +05:30
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+# LLM Wiki Agent — Schema & Workflow Instructions
+
+This wiki is maintained entirely by Gemini CLI. No API key or Python scripts needed — just open this repo with `gemini` and talk to it.
+
+## How to Use
+
+Describe what you want in plain English:
+- *"Ingest this file: raw/papers/my-paper.md"*
+- *"What does the wiki say about transformer models?"*
+- *"Check the wiki for orphan pages and contradictions"*
+- *"Build the knowledge graph"*
+
+Or use shorthand triggers:
+- `ingest <file>` → runs the Ingest Workflow
+- `query: <question>` → runs the Query Workflow
+- `lint` → runs the Lint Workflow
+- `build graph` → runs the Graph Workflow
+
+---
+
+## Directory Layout
+
+```
+raw/          # Immutable source documents — never modify these
+wiki/         # Agent owns this layer entirely
+  index.md    # Catalog of all pages — update on every ingest
+  log.md      # Append-only chronological record
+  overview.md # Living synthesis across all sources
+  sources/    # One summary page per source document
+  entities/   # People, companies, projects, products
+  concepts/   # Ideas, frameworks, methods, theories
+  syntheses/  # Saved query answers
+graph/        # Auto-generated graph data
+tools/        # Optional standalone Python scripts
+```
+
+---
+
+## Page Format
+
+Every wiki page uses this frontmatter:
+
+```yaml
+---
+title: "Page Title"
+type: source | entity | concept | synthesis
+tags: []
+sources: []
+last_updated: YYYY-MM-DD
+---
+```
+
+Use `[[PageName]]` wikilinks to link to other wiki pages.
+
+---
+
+## Ingest Workflow
+
+Triggered by: *"ingest <file>"*
+
+1. Read the source document fully
+2. Read `wiki/index.md` and `wiki/overview.md` for current wiki context
+3. Write `wiki/sources/<slug>.md` (source page format below)
+4. Update `wiki/index.md` — add entry under Sources
+5. Update `wiki/overview.md` — revise synthesis if warranted
+6. Update/create entity and concept pages
+7. Flag contradictions with existing wiki content
+8. Append to `wiki/log.md`: `## [YYYY-MM-DD] ingest | <Title>`
+
+### Source Page Format
+
+```markdown
+---
+title: "Source Title"
+type: source
+tags: []
+date: YYYY-MM-DD
+source_file: raw/...
+---
+
+## Summary
+2–4 sentence summary.
+
+## Key Claims
+- Claim 1
+
+## Key Quotes
+> "Quote here"
+
+## Connections
+- [[EntityName]] — how they relate
+
+## Contradictions
+- Contradicts [[OtherPage]] on: ...
+```
+
+---
+
+## Query Workflow
+
+Triggered by: *"query: <question>"*
+
+1. Read `wiki/index.md` — identify relevant pages
+2. Read those pages
+3. Synthesize answer with `[[PageName]]` citations
+4. Offer to save as `wiki/syntheses/<slug>.md`
+
+---
+
+## Lint Workflow
+
+Triggered by: *"lint"*
+
+Check for: orphan pages, broken links, contradictions, stale content, missing entity pages, data gaps.
+
+---
+
+## Graph Workflow
+
+Triggered by: *"build graph"*
+
+Try `python tools/build_graph.py --open` first. If unavailable, build graph.json and graph.html manually from wikilinks.
+
+---
+
+## Naming Conventions
+
+- Source slugs: `kebab-case`
+- Entity/Concept pages: `TitleCase.md`
+
+## Log Format
+
+`## [YYYY-MM-DD] <operation> | <title>`