docs: update nested READMEs in tools/, documents/, agents/ to reflect current contents

agents/README.md

@@ -1,17 +1,34 @@
 # Agents
 
-Per-agent configuration, context, and notes for AI tools working in this environment.
+Per-agent configuration, context, and notes for AI coding tools working in this environment.
 
-Each file is tailored to a specific AI coding agent — its quirks, best practices, and how to get the most out of it in Jacob Mathison's stack.
+Each file is tailored to a specific agent — workspace paths, behavioral rules, tool patterns, and environment-specific tips.
 
 ## Agents
 
-| File | Agent | Notes |
+| File | Agent | Status |
-|------|-------|-------|
+|------|-------|--------|
-| [`claude.md`](./claude.md) | Anthropic Claude (Claude Code / API) | |
+| [`claude.md`](./claude.md) | Anthropic Claude (Claude Code / API) | ✅ Filled |
-| [`cursor.md`](./cursor.md) | Cursor IDE AI | |
+| [`cursor.md`](./cursor.md) | Cursor IDE AI | 🔲 Blank |
-| [`codex.md`](./codex.md) | OpenAI Codex / ChatGPT with code access | |
+| [`codex.md`](./codex.md) | OpenAI Codex / ChatGPT with code access | 🔲 Blank |
 
 ## How to Use
 
-When starting a session with one of these agents, point it at the relevant file alongside the surface guides (`gitea.llm.md`, `github.llm.md`, `aws-cli.llm.md`) for full context.
+Point your agent at the relevant file at session start alongside the surface guides in `tools/` for full context:
+
+```
+tools/gitea.llm.md      → local git access
+tools/github.llm.md     → GitHub access
+tools/aws-cli.llm.md    → AWS access
+tools/tailscale.llm.md  → network / machines
+tools/vault.llm.md      → secrets
+tools/k8s.llm.md        → local services
+tools/local-llm.llm.md  → local LLMs
+tools/claude-cli.md     → Claude Code CLI reference
+tools/codex-cli.md      → Codex CLI reference
+tools/cursor-cli.md     → Cursor reference
+```
+
+## Adding a New Agent
+
+Create `<agent-slug>.md` in this folder, then update `agents/README.md` and `manifest.json`.

documents/README.md

@@ -2,11 +2,19 @@
 
 Reference documents, specs, and written context for AI agents working in this environment.
 
-> This folder is a placeholder — add project specs, architecture docs, onboarding docs, and written context here as they are developed.
+## Contents
 
-## Intended Contents
+| File | What it covers |
+|------|---------------|
+| [`onboarding.md`](./onboarding.md) | Step-by-step start-here checklist for new agents — network, git, AWS, k8s, red lines |
+| [`machines.md`](./machines.md) | Full machine inventory — Tabitha, Orson, Ozymandias, Hunter, GoatLord — hardware, roles, connection patterns |
 
+## Adding a New Document
+
+Create a `<name>.md` file in this folder, then update `documents/README.md` and `manifest.json`.
+
+Intended future contents:
 - Project specifications and requirements
 - Architecture overviews
-- Onboarding documents for specific projects
+- Coding standards and conventions
 - Meeting notes or decision logs relevant to AI context

tools/README.md

@@ -1,16 +1,30 @@
 # Tools
 
-Access guides for the third-party services and platforms AI agents need to work with in this environment.
+Access guides for the external services, platforms, and CLI tools AI agents need to work with in this environment.
 
 Each file covers one surface — authentication, available resources, and common CLI/API patterns.
 
 ## Guides
 
+### Infrastructure & Services
+
 | File | Surface | Key Info |
 |------|---------|----------|
 | [`gitea.llm.md`](./gitea.llm.md) | Local Gitea (self-hosted git) | `http://100.79.253.19:3000` · PAT auth · Tailscale required |
 | [`github.llm.md`](./github.llm.md) | GitHub | MathisonProjects + silmaai · PAT in `credentials/secrets.env` |
 | [`aws-cli.llm.md`](./aws-cli.llm.md) | AWS | Account `567637986724` · S3 · Amplify · CloudFront · Lambda |
+| [`tailscale.llm.md`](./tailscale.llm.md) | Tailscale network | Machine IPs · kittens bridge · connectivity checks |
+| [`vault.llm.md`](./vault.llm.md) | HashiCorp Vault | `localhost:18200` · token `devroot` · all secret paths listed |
+| [`k8s.llm.md`](./k8s.llm.md) | Kubernetes (silma-ai) | Service map · ports · kubectl patterns · storage notes |
+
+### AI Tools & Models
+
+| File | Tool | Key Info |
+|------|------|----------|
+| [`local-llm.llm.md`](./local-llm.llm.md) | Local LLMs (llama.cpp) | Gemma-4-E4B @ `localhost:8080` · Gemma-4-26B @ `localhost:8081` |
+| [`claude-cli.md`](./claude-cli.md) | Claude Code CLI | Install · commands · flags · MCP · local LLM wiring |
+| [`codex-cli.md`](./codex-cli.md) | OpenAI Codex CLI | Install · approval modes · AGENTS.md · local LLM wiring |
+| [`cursor-cli.md`](./cursor-cli.md) | Cursor IDE/CLI | Agent mode · rules · MCP · local LLM · Gitea integration |
 
 ## Adding a New Tool
 
@@ -21,4 +35,4 @@ Create a new `<toolname>.llm.md` file in this folder following the same pattern:
 4. Common CLI/API patterns
 5. Notes for AI agents
 
-Then update `Tools/README.md` and the root `manifest.json`.
+Then update `tools/README.md`, `README.md` (root), `llm.txt`, and `manifest.json`.