tuannv0069/claude-doc-genome

init-project

purpose

Bootstrap a new project's agent documentation system from a portable bundle in one shot. After init the project self-maintains using the deployed standard (doc-organization.md §8.3 decision tree + portable meta-standards). init runs once per project; update may be re-run later at that project to pull newer portable files from the bundle (3-way safe merge — never clobbers un-promoted local edits). check/promote maintain the bundle itself and run only at this master repo.

dependencies

• ./portable/rules/ — 7 portable rules (always-loaded + path-scoped)
• ./portable/agent-guide/ — five-why.md, markdown.md, mermaid.md, orchestration-policy.md, worktree.md (deploy to docs/agent-guide/general/)
• ./portable/skills/ — skill-designer/, skill-writer/, document-writer/ (whole trees)
• ./portable/agents/ — skill-writer-auditor.md
• ./templates/ — CLAUDE.md.tpl, agent-guide/index.md.tpl, docs/index.md.tpl
• ./VERSION — bundle version, bumped on every promote
• scripts/update.mjs (repo root) — engine for the update mode (3-way bundle→live merge); scripts/sync-version.mjs — version single-source sync

modes

invocation	runs where	action
/init-project	new project	deploy bundle (workflow below)
/init-project check	master repo	sha256 compare bundle ↔ live per §map → report drift
/init-project promote	master repo	copy live → bundle for every mapped file, bump VERSION
/init-project update	initialized project	pull newer portable files bundle → live, 3-way safe (manifest ↔ live ↔ bundle); skip conflicts (workflow below)

workflow (init — new project)

1. Scan project: detect stack + optional modules per ## module matrix signal column. Output: proposed module set + discovered slot values.
2. Interview: confirm proposed module set; ask slots not scannable (dev ports in use, scope ownership, doc language). Unanswerable slot → leave TODO marker, never invent a value; module uncertain → skip it.
3. Copy portable/ verbatim: portable/rules/* → .claude/rules/; portable/agent-guide/* → docs/agent-guide/general/; portable/skills/* → .claude/skills/; portable/agents/* → .claude/agents/.
4. Render templates: fill {{slots}} from interview into CLAUDE.md, docs/agent-guide/index.md, docs/index.md; missing slot → keep TODO marker.
5. Generate optional rules: for each confirmed optional module, write a project-fitted rule into docs/agent-guide/general/ per rule-writing-standards, and append its trigger line to CLAUDE.md in the same step — no hardcoded template.
6. Write manifest .claude/init-manifest.json: { version, deployedAt, files:[{path,sha256}], templates:[{path,sha256}], modules:[...] } (provenance; files[] read by update for 3-way drift detection — keep sha256 accurate; templates[] records the .tpl sha each rendered file was built from — path = template path relative to templates/ e.g. CLAUDE.md.tpl, used by update to WARN when a template changed since deploy).
7. Verify: every deployed file is at the correct tier; every rule/agent-guide file carries scope: frontmatter; CLAUDE.md within token budget; every behavior-affecting on-demand file has a trigger line or router entry (reachability, file→trigger); every MUST Read trigger in CLAUDE.md resolves to a deployed file (reachability, trigger→file — no dead trigger); no unrendered {{slot}} remains except intentional TODO markers. Done = checklist passes + manifest written.

bundle ↔ live map (check / promote — master repo; update — initialized project)

bundle path	live path
portable/rules/*	.claude/rules/*
portable/agent-guide/*	docs/agent-guide/general/*
portable/skills/*	.claude/skills/*
portable/agents/*	.claude/agents/*

• check: sha256 each pair → list mismatches. Default update direction is live → bundle (promote); fix live first, then promote.
• promote: copy live → bundle for every mapped file, then bump the version via node scripts/sync-version.mjs set <x.y.z> (writes canonical VERSION + mirrors it into .claude-plugin/* and the README badge).

workflow (update — initialized project)

Direction bundle → live (reverse of promote). Touches only the verbatim portable set; rendered phenotype (CLAUDE.md, index.md, project-authored guides) is out of scope. Invoke update.mjs by its path inside the installed plugin (it self-locates the bundle from its own location); --project is the initialized project root and defaults to the current directory.

1. Dry-run: node <plugin>/scripts/update.mjs --project <project-root> → review the ADD / UPDATE / CONFLICT plan and the version delta.
2. Resolve every CONFLICT first — a conflict = a portable file edited locally since deploy. Promote it upstream (so the improvement enters the bundle) or overwrite manually after review. Never blind-overwrite.
3. Apply: node <plugin>/scripts/update.mjs --apply --project <project-root> → writes ADD + UPDATE, skips conflicts, refreshes manifest version + files[].sha256.
4. Additive + in-place only — update never deletes: a file removed from the bundle stays in the project, and a file deleted locally is re-added. Prune those manually if needed.
   • templates/* (CLAUDE.md, index.md — rendered phenotype) are never overwritten: their slots hold project-specific values. update only emits a WARN when a .tpl changed since deploy (sha vs manifest.templates[]); re-render manually (diff .tpl vs live, re-apply structural changes, keep slot values) or re-run /init-project. The WARN persists until the next init re-records the template sha.
5. Exit code: 0 = up-to-date or applied cleanly; 1 = conflicts remain; 2 = setup error (no manifest → project was not init'd by this plugin).

module matrix

module	includes	deploy when	scan signal (examples, not exhaustive)
core	portable/* (all 4 groups) + 3 templates	always	—
runtime	agent-guide/general/local-runtime.md + CLAUDE.md trigger (skill writes per scan, step 5)	project self-runs a dev server	package.json dev/start scripts, launchSettings.json, vite/next/dotnet/django/cargo config
e2e	agent-guide/general/<tool>.md (named after detected tool) + CLAUDE.md trigger (step 5)	project has E2E browser tests	playwright/cypress/selenium dep, e2e/ folder, E2E config

• Optional module deploys only when scan confirms OR user confirms at interview — uncertain → skip.
• Git: minimal guardrail (commit only on request, never push) ships in CLAUDE.md.tpl; detailed policy is scope: project — project writes docs/agent-guide/general/git.md on demand, adding its trigger line in the same commit (reachability — never a trigger pointing at a missing file).
• A skipped module needed later → project writes the rule itself per the deployed standard. New module enters the bundle only via promote after a real project battle-tests the pattern.

independence rules

• Skill runs once per project; deployed files reference no file of this master repo; project rules never name this skill.
• Self-contained except the bundle↔live map above, which executes only at the master repo for check/promote.

examples

✅ scan finds package.json with "dev" script → propose runtime module → step 5 writes
   general/local-runtime.md + appends "self-run dev server → MUST Read ..." to CLAUDE.md
❌ deploy runtime module with no scan signal and no interview confirm (guessed module)

✅ /init-project check → "MISMATCH: portable/rules/doc-organization.md != .claude/rules/doc-organization.md"
   → fix live first → /init-project promote
❌ edit portable/* directly then init a new project (bundle diverges silently from live)

reference files

• bundle: ./portable/**
• templates: ./templates/**
• version: ./VERSION