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

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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>
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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`

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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>`

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- **`wiki/`** — Claude-maintained markdown pages (Claude writes, you read) - **`wiki/`** — Claude-maintained markdown pages (Claude writes, you read)
- **`graph/`** — auto-generated knowledge graph visualization - **`graph/`** — auto-generated knowledge graph visualization
## Quick Start — Claude Code (no API key needed) ## Quick Start — Any Coding Agent (no API key needed)
Open this repo in [Claude Code](https://claude.ai/code): Works with Claude Code, Codex, OpenCode, Gemini CLI, and any agent that reads a config file from the repo root.
| Agent | Config file read automatically |
|---|---|
| [Claude Code](https://claude.ai/code) | `CLAUDE.md` + `.claude/commands/` |
| [OpenAI Codex](https://openai.com/codex) | `AGENTS.md` |
| OpenCode / Pear AI | `AGENTS.md` |
| [Gemini CLI](https://github.com/google-gemini/gemini-cli) | `GEMINI.md` |
| Any other agent | Point it at `AGENTS.md` or `README.md` |
```bash ```bash
git clone https://github.com/SamurAIGPT/GPT-Agent.git git clone https://github.com/SamurAIGPT/GPT-Agent.git
cd GPT-Agent cd GPT-Agent
claude # opens Claude Code in this repo
claude # Claude Code
codex # OpenAI Codex
opencode # OpenCode
gemini # Gemini CLI
``` ```
Claude Code reads `CLAUDE.md` automatically. Then just talk to it: Each agent reads its config file and follows the same workflows. Then talk to it:
``` ```
# Drop a source into raw/ first, then: # Claude Code slash commands:
/wiki-ingest raw/articles/my-article.md /wiki-ingest raw/articles/my-article.md
/wiki-query what are the main themes across all sources? /wiki-query what are the main themes across all sources?
/wiki-lint /wiki-lint
/wiki-graph /wiki-graph
```
Or in plain English: *"Ingest this paper"*, *"What does the wiki say about X?"*, *"Check for contradictions"* # Any agent (plain English):
"Ingest this paper: raw/papers/my-paper.md"
"What does the wiki say about X?"
"Check for contradictions"
"Build the knowledge graph"
```
## Quick Start — Standalone Python (requires API key) ## Quick Start — Standalone Python (requires API key)