@@ -6,7 +6,7 @@ alwaysApply: true
 
 > **STOP.** Before you call Grep, Glob, SemanticSearch, or Read to answer a **structural** question about this repository — query the Codemap SQLite index first. This is not optional when the question matches a trigger pattern below.
 
-A local database (default **`.codemap.db`**) indexes structure: symbols, imports, exports, components, dependencies, markers, CSS variables, CSS classes, CSS keyframes.
+A local database (default **`.codemap/index.db`**) indexes structure: symbols, imports, exports, components, dependencies, markers, CSS variables, CSS classes, CSS keyframes. The `.codemap/` directory holds every codemap-managed file (`index.db` + WAL/SHM, `audit-cache/`, project `recipes/`, `config.{ts,js,json}`, self-managed `.gitignore`); override the dir with `--state-dir <path>` or `CODEMAP_STATE_DIR`. The `.codemap/.gitignore` is **codemap-managed and reconciled on every boot** (`ensureStateGitignore`) — bumping its canonical body in a PR auto-applies on every consumer's next run.
 
 **This file** is for **developing Codemap** in this clone. **End users** of the published package get the agent rule from **`templates/agents/`** (via **`codemap agents init`**). **Generic defaults:** SQL and triggers stay project-agnostic — **edit** this rule for repo-specific paths and queries.
 
@@ -51,7 +51,7 @@ actions:
 
 Validation: SQL is rejected at load time if it starts with DML/DDL (DELETE/DROP/UPDATE/etc.); the runtime `PRAGMA query_only=1` is the parser-proof backstop.
 
-**Baselines** (`query_baselines` table inside `.codemap.db`, no parallel JSON files): `--save-baseline[=<name>]` snapshots a result set; `--baseline[=<name>]` diffs the current result against it (added / removed rows; identity = `JSON.stringify(row)`). Name defaults to the `--recipe` id; ad-hoc SQL needs an explicit `=<name>`. Survives `--full` and SCHEMA bumps.
+**Baselines** (`query_baselines` table inside `.codemap/index.db`, no parallel JSON files): `--save-baseline[=<name>]` snapshots a result set; `--baseline[=<name>]` diffs the current result against it (added / removed rows; identity = `JSON.stringify(row)`). Name defaults to the `--recipe` id; ad-hoc SQL needs an explicit `=<name>`. Survives `--full` and SCHEMA bumps.
 
 **Audit (`bun src/index.ts audit`)**: structural-drift command; emits `{head, deltas: {files, dependencies, deprecated}}` (each delta carries its own `base` metadata). Three mutually-exclusive snapshot sources: `--base <ref>` materialises a git committish via `git worktree add` to a sha-keyed cache under `.codemap/audit-cache/`, reindexes a temp DB, then diffs (sub-100ms second run; requires git; `base.source: "ref"`); `--baseline <prefix>` auto-resolves `<prefix>-files` / `<prefix>-dependencies` / `<prefix>-deprecated` from saved `query_baselines` entries (`base.source: "baseline"`); `--<delta>-baseline <name>` is the explicit per-delta override (composes with both). v1 ships no `verdict` / threshold config — consumers compose `--json` + `jq` for CI exit codes. Auto-runs an incremental index before the diff (use `--no-index` to skip for frozen-DB CI).
 
 
@@ -41,11 +41,11 @@ Replace placeholders (`'...'`) with your module path, file glob, or symbol name.
 - **`--summary`** — counts only. With **`--json`**: **`{"count": N}`**. With **`--group-by`**: **`{"group_by": "<mode>", "groups": [{key, count}]}`**.
 - **`--changed-since <ref>`** — post-filter rows by **`path`** / **`file_path`** / **`from_path`** / **`to_path`** / **`resolved_path`** against **`git diff --name-only <ref>...HEAD ∪ git status --porcelain`**. Rows with no recognised path column pass through.
 - **`--group-by owner|directory|package`** — partition into buckets and emit **`{"group_by", "groups": [{key, count, rows}]}`**. **`owner`** reads CODEOWNERS (last matching rule wins); **`directory`** is the first path segment; **`package`** uses **`package.json`** **`workspaces`** or **`pnpm-workspace.yaml`**. **Mutually exclusive with `--save-baseline` / `--baseline`.**
-- **`--save-baseline[=<name>]`** — snapshot the result rows to the **`query_baselines`** table inside `.codemap.db` (no parallel JSON files; survives `--full` and SCHEMA bumps). Name defaults to the `--recipe` id; ad-hoc SQL needs an explicit `=<name>`. Re-saving with the same name overwrites in place.
+- **`--save-baseline[=<name>]`** — snapshot the result rows to the **`query_baselines`** table inside `<state-dir>/index.db` (default `.codemap/index.db`; no parallel JSON files; survives `--full` and SCHEMA bumps). Name defaults to the `--recipe` id; ad-hoc SQL needs an explicit `=<name>`. Re-saving with the same name overwrites in place.
 - **`--baseline[=<name>]`** — diff the current result against the saved baseline. Output `{baseline:{...}, current_row_count, added: [...], removed: [...]}` (with `--json`) or a two-section terminal dump. Identity = per-row multiset equality (canonical `JSON.stringify` keyed frequency map; duplicates preserved). Pair with `--summary` for `{baseline:{...}, current_row_count, added: N, removed: N}`. **Mutually exclusive with `--group-by`.**
 - **`--baselines`** lists saved baselines (no `rows_json` payload); **`--drop-baseline <name>`** deletes one. Both reject every other flag — they're list-only / drop-only operations.
 - **Per-row recipe `actions`** — recipes that define an **`actions: [{type, auto_fixable?, description?}]`** template append it to every row in **`--json`** output (recipe-only; ad-hoc SQL never carries actions). Under `--baseline`, actions attach to the **`added`** rows only (the rows the agent should act on). Inspect via **`--recipes-json`**.
-- **Project-local recipes** — drop **`<id>.sql`** (and optional **`<id>.md`** for description body + actions) into **`<projectRoot>/.codemap/recipes/`** to make team-internal SQL a first-class CLI verb. `--recipes-json` and the `codemap://recipes` MCP resource list project recipes alongside bundled ones with **`source: "bundled" | "project"`** discriminating them. Project recipes win on id collision; entries that override a bundled id carry **`shadows: true`** so agents reading the catalog at session start know when a recipe behaves differently from the documented bundled version. `<id>.md` supports YAML frontmatter for the per-row action template — **block-list shape only** (loader's hand-rolled parser; no inline-flow `[{...}]`): `---\nactions:\n  - type: my-verb\n    auto_fixable: false\n    description: "..."\n---`. Validation: SQL is rejected at load time if it starts with DML/DDL (DELETE/DROP/UPDATE/etc.); the runtime `PRAGMA query_only=1` is the parser-proof backstop. `.codemap.db` is gitignored; **`.codemap/recipes/` is NOT** — recipes are git-tracked source code authored for human review.
+- **Project-local recipes** — drop **`<id>.sql`** (and optional **`<id>.md`** for description body + actions) into **`<state-dir>/recipes/`** (default `<projectRoot>/.codemap/recipes/`) to make team-internal SQL a first-class CLI verb. `--recipes-json` and the `codemap://recipes` MCP resource list project recipes alongside bundled ones with **`source: "bundled" | "project"`** discriminating them. Project recipes win on id collision; entries that override a bundled id carry **`shadows: true`** so agents reading the catalog at session start know when a recipe behaves differently from the documented bundled version. `<id>.md` supports YAML frontmatter for the per-row action template — **block-list shape only** (loader's hand-rolled parser; no inline-flow `[{...}]`): `---\nactions:\n  - type: my-verb\n    auto_fixable: false\n    description: "..."\n---`. Validation: SQL is rejected at load time if it starts with DML/DDL (DELETE/DROP/UPDATE/etc.); the runtime `PRAGMA query_only=1` is the parser-proof backstop. `.codemap/index.db` is gitignored; **`.codemap/recipes/` is NOT** — recipes are git-tracked source code authored for human review.
 
 **Audit (`bun src/index.ts audit`)** — separate top-level command for structural-drift verdicts. Composes B.6 baselines into a per-delta `{head, deltas}` envelope; v1 ships `files` / `dependencies` / `deprecated`. Two snapshot-source shapes:
 
@@ -79,7 +79,7 @@ Each emitted delta carries its own `base` metadata so mixed-baseline audits are
 
 - **`codemap://recipes`** — full catalog JSON (same as `--recipes-json`). Each entry carries `source: "bundled" | "project"` and `shadows: true` on project entries that override a bundled recipe id. Read this at session start so you know when a `--recipe foo` call will run a project override instead of the documented bundled version.
 - **`codemap://recipes/{id}`** — single recipe `{id, description, body?, sql, actions?, source, shadows?}`. Replaces `--print-sql <id>`.
-- **`codemap://schema`** — DDL of every table in `.codemap.db` (queried live from `sqlite_schema`).
+- **`codemap://schema`** — DDL of every table in `.codemap/index.db` (queried live from `sqlite_schema`).
 - **`codemap://skill`** — full text of bundled `templates/agents/skills/codemap/SKILL.md`. Agents that don't preload the skill at session start can fetch it here.
 
 **Implementation:** `src/cli/cmd-mcp.ts` (CLI shell — argv + lifecycle) + `src/application/mcp-server.ts` (transport — SDK glue). Tool bodies live in `src/application/tool-handlers.ts` (pure transport-agnostic — same handlers `codemap serve` dispatches over HTTP); resource fetchers in `src/application/resource-handlers.ts`. Mirrors the `cmd-audit.ts ↔ audit-engine.ts` seam. `--changed-since` git lookups are memoised per `(root, ref)` pair across batch items so a `query_batch` of N items sharing the same ref does one git invocation, not N.
 
@@ -0,0 +1,38 @@
+---
+"@stainless-code/codemap": minor
+---
+
+`.codemap/` directory consolidation + self-healing files. Every codemap-managed path lives under a single configurable state directory (default `.codemap/`, override via `--state-dir <path>` or `CODEMAP_STATE_DIR`). Cleans up the dual-pattern surface (`<root>/.codemap.db` + `<root>/.codemap/<thing>/`) that's been growing with every cache PR; collapses the user `.gitignore` patching surface to zero.
+
+**New layout:**
+
+```
+<root>/
+└── .codemap/                 ← override via --state-dir / CODEMAP_STATE_DIR
+    ├── .gitignore            ← codemap-managed (self-healing); tracked
+    ├── config.{ts,js,json}   ← was <root>/codemap.config.*; tracked
+    ├── recipes/              ← user-authored SQL; tracked (existing)
+    ├── index.db              ← was .codemap.db
+    ├── index.db-shm          ← was .codemap.db-shm
+    ├── index.db-wal          ← was .codemap.db-wal
+    └── audit-cache/          ← was .codemap/audit-cache/ (existing)
+```
+
+**Self-healing files (D11):** `<state-dir>/.gitignore` and `<state-dir>/config.json` are owned by idempotent `ensure*` reconcilers (`src/application/state-dir.ts`, `src/application/state-config.ts`) that run on every codemap boot — read → validate → reconcile → write only on drift. **The setup logic IS the migration**: future codemap versions add new generated artifacts to `STATE_GITIGNORE_BODY` (or extend the Zod schema), and every consumer's project repairs itself on the next `codemap` invocation. No more per-feature `.gitignore` patching in `agents-init.ts`.
+
+**Pre-v1 — no migration shim:**
+
+- `<root>/.codemap.db` → `<state-dir>/index.db` (rename basename)
+- `<root>/codemap.config.{ts,json}` → `<state-dir>/config.{ts,js,json}` (move file)
+- Existing dev clones: `rm .codemap.db .codemap.db-shm .codemap.db-wal` once and re-index; move `codemap.config.*` into `.codemap/` (or set `--config <old-path>` to keep using the legacy location explicitly).
+
+**New flags + env:**
+
+- `--state-dir <path>` — override the state directory (resolves relative to project root).
+- `CODEMAP_STATE_DIR` — same, env-var form.
+
+**Internal refactor:** new `src/cli/bootstrap-codemap.ts` extracts the `loadUserConfig + resolveCodemapConfig + initCodemap + configureResolver` dance from 9 cmd-\* files into one helper that also runs the self-healing reconcilers. Adding a new self-healing file is now a one-line addition there.
+
+Inspired by flowbite-react's `.flowbite-react/.gitignore` + `setup-*` pattern; expressed in codemap's own conventions (`ensure*` reconcilers, Zod schema as `z.infer` source of truth, pure `{before, after, written}` return shapes for testability).
+
+Plan: PR #53 (merged). Implementation: PR #54.
@@ -0,0 +1,7 @@
+# codemap-managed — edits will be overwritten by `ensureStateGitignore`.
+# Blacklist of generated artifacts; tracked sources (recipes/, config.*)
+# default to tracked. Bump alongside any new cache (Rule 9 analogue).
+index.db
+index.db-shm
+index.db-wal
+audit-cache/
@@ -1,6 +1,4 @@
 node_modules/
-.codemap.*
-.codemap/audit-cache/
 .DS_Store
 dist/
 *.tgz