Modularize Agents Md

Phase 1: Audit

Read the current AGENTS.md and understand the project structure.

1. List all top-level sections in the AGENTS.md
2. Map each section to the source code it describes
3. Categorize each section:
   • Root AGENTS.md — environment setup, code style, project structure (folder-level only), external dependencies, links to sub-docs
   • Folder-level AGENTS.md — lightweight hub for a directory: architecture overview, links to per-component docs
   • Per-component .md — design, API checklists, dependencies, used-by, gotchas for a specific module
   • Skills — procedural workflows that are reusable (e.g. adding a new model, running experiments)
   • Global AGENTS.md — truly cross-project knowledge (general language gotchas, environment info). Lives in the agent harness's global config.
4. Identify sections currently in the wrong place (e.g. project-specific gotchas in global AGENTS.md, module details in root)

Present your audit and proposed file tree to the user. Confirm before proceeding.

Phase 2: Create Root and Hub Files

Rewrite the root AGENTS.md to be lean:

• Keep: environment setup (package manager, test/lint commands), code style, external dependencies, repo-level metadata
• Replace detailed file listings with one line per top-level folder + a link to that folder's AGENTS.md
• Add a Skills section listing available project skills and a note about skill discovery for different agent harnesses
• Move anything not project-specific (SLURM, general language gotchas) to the global AGENTS.md

For each major directory (src/<package>/, tests/, examples/, docs/, models/), create a lightweight AGENTS.md:

• Brief purpose statement
• Architecture overview (for code directories — inheritance trees, composition patterns)
• Links to per-component .md files
• Cross-cutting concerns (shared conventions, tokenization ecosystems)
• Known tech debt / stale code

Keep hubs under ~60 lines. They're navigation aids, not documentation.

Phase 3: Create Per-Component Design Docs

For each logical component (one .py file or a tightly coupled group), create a <component>.md alongside the source. Work one at a time — show the user each extraction for feedback.

Required sections

# <Component Name> — Design Notes

<1-2 line purpose statement>

## Dependencies
- [other_component.md](relative/link) — what this component imports/relies on

## Used By
- [consumer.md](relative/link) — what imports/uses this component

## <Design content>
- API checklists (abstract vs concrete methods for ABCs)
- Key method signatures and contracts
- Pipeline walkthroughs for complex flows

## Maintenance
<Link to relevant skill if changes here should trigger a skill update>

## Gotchas
- Concrete, actionable traps with fixes

Guidelines

• Tables for API checklists — abstract methods, overridable defaults, concrete methods
• Code blocks for pipelines — show the flow (e.g. get_log_probs pipeline)
• Cross-link liberally — every dependency and consumer should be a clickable relative link
• Preserve existing knowledge — don't lose gotchas or design notes from the original AGENTS.md. Every bullet should land somewhere.
• No duplication of docstrings — the .md captures working knowledge (how things connect, why decisions were made, what breaks). The docstring explains the API.
• Models get their own directories — each model in models/<name>/ with its own .md, even if it's currently a single file. Scales better as models are added.
• Don't over-split — if two things are always edited together (e.g. TransitionModel and LogitFormatter in the same .py), they belong in the same .md

Phase 4: Extract Skills and Clean Up

Skills: Look for procedural knowledge — multi-step processes an agent would follow. For each, create a skill in .agents/skills/<name>/SKILL.md with phases, decision trees, and gotcha checklists. Add maintenance notes in relevant component .md files pointing to skills that need updating when the component changes.

Global AGENTS.md cleanup: Move project-specific gotchas out. Keep truly cross-project knowledge. Generalize any gotchas that have broader applicability (remove project-specific references from the description).

Verify:

1. Every section from the original AGENTS.md landed somewhere — no knowledge lost
2. All relative links point to real files
3. Root and hub files are under ~60 lines each
4. Per-component docs have Dependencies, Used By, and Gotchas sections
5. Usage counters ([×N]) transferred from original to destination files