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 your coding agent. No API key or Python scripts needed — just open this repo in Codex, OpenCode, or any agent that reads this file, 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 (require ANTHROPIC_API_KEY)
+```
+
+---
+
+## Page Format
+
+Every wiki page uses this frontmatter:
+
+```yaml
+---
+title: "Page Title"
+type: source | entity | concept | synthesis
+tags: []
+sources: []       # list of source slugs that inform this page
+last_updated: YYYY-MM-DD
+---
+```
+
+Use `[[PageName]]` wikilinks to link to other wiki pages.
+
+---
+
+## Ingest Workflow
+
+Triggered by: *"ingest <file>"*
+
+Steps (in order):
+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` — use the source page format below
+4. Update `wiki/index.md` — add entry under Sources section
+5. Update `wiki/overview.md` — revise synthesis if warranted
+6. Update/create entity pages for key people, companies, projects mentioned
+7. Update/create concept pages for key ideas and frameworks discussed
+8. Flag any contradictions with existing wiki content
+9. 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
+- Claim 2
+
+## Key Quotes
+> "Quote here" — context
+
+## Connections
+- [[EntityName]] — how they relate
+- [[ConceptName]] — how it connects
+
+## Contradictions
+- Contradicts [[OtherPage]] on: ...
+```
+
+---
+
+## Query Workflow
+
+Triggered by: *"query: <question>"*
+
+Steps:
+1. Read `wiki/index.md` to identify relevant pages
+2. Read those pages
+3. Synthesize an answer with inline citations as `[[PageName]]` wikilinks
+4. Ask the user if they want the answer filed as `wiki/syntheses/<slug>.md`
+
+---
+
+## Lint Workflow
+
+Triggered by: *"lint"*
+
+Check for:
+- **Orphan pages** — wiki pages with no inbound `[[links]]` from other pages
+- **Broken links** — `[[WikiLinks]]` pointing to pages that don't exist
+- **Contradictions** — claims that conflict across pages
+- **Stale summaries** — pages not updated after newer sources
+- **Missing entity pages** — entities mentioned in 3+ pages but lacking their own page
+- **Data gaps** — questions the wiki can't answer; suggest new sources
+
+Output a lint report and ask if the user wants it saved to `wiki/lint-report.md`.
+
+---
+
+## Graph Workflow
+
+Triggered by: *"build graph"*
+
+First try: `python tools/build_graph.py --open`
+
+If Python/deps unavailable, build manually:
+1. Search for all `[[wikilinks]]` across wiki pages
+2. Build nodes (one per page) and edges (one per link)
+3. Infer implicit relationships not captured by wikilinks — tag `INFERRED` with confidence score; low confidence → `AMBIGUOUS`
+4. Write `graph/graph.json` with `{nodes, edges, built: date}`
+5. Write `graph/graph.html` as a self-contained vis.js visualization
+
+---
+
+## Naming Conventions
+
+- Source slugs: `kebab-case` matching source filename
+- Entity pages: `TitleCase.md` (e.g. `OpenAI.md`, `SamAltman.md`)
+- Concept pages: `TitleCase.md` (e.g. `ReinforcementLearning.md`, `RAG.md`)
+
+## Index Format
+
+```markdown
+# Wiki Index
+
+## Overview
+- [Overview](overview.md) — living synthesis
+
+## Sources
+- [Source Title](sources/slug.md) — one-line summary
+
+## Entities
+- [Entity Name](entities/EntityName.md) — one-line description
+
+## Concepts
+- [Concept Name](concepts/ConceptName.md) — one-line description
+
+## Syntheses
+- [Analysis Title](syntheses/slug.md) — what question it answers
+```
+
+## Log Format
+
+`## [YYYY-MM-DD] <operation> | <title>`
+
+Operations: `ingest`, `query`, `lint`, `graph`