fix(audit-base): address all 6 CodeRabbit review comments + 2 nitpicks

Threads (all 6 actionable, no hallucinations):

1. .agents/rules + templates: stale 'B.6' spec leak → 'query_baselines entries' (consistent terminology)
2. audit-engine.ts: process-level mutex (_reindexChain promise queue) around makeWorktreeReindex's runtime-singleton swap. Concurrent HTTP/MCP audits no longer interleave initCodemap/configureResolver state. Long-term cleanup (runCodemapIndex takes explicit context) tracked separately.
3. audit-worktree.test.ts: commitFiles fixture now checks git commit exit code; throws with stderr on failure (was silently passing against previous commit)
4. audit-worktree.ts: tmpName gains randomUUID() suffix (defensive against cross-process races; in-process serialised by mutex from #2)
5. audit-worktree.ts: evictIfOverLimits accepts protectPath; populateWorktree passes finalPath so the freshly-populated entry can't evict itself when it alone exceeds MAX_CACHE_BYTES. New test covers the protect path.
6. mcp-server.ts + .agents/skills + templates: rephrased 'three mutually exclusive sources' to 'two mutually exclusive PRIMARY sources + optional per-delta overrides' (matches handleAudit's actual exclusivity rule)

Nitpicks:
- fallow.md status: 'v1 + v1.x partial shipped' → 'v1 + v1.x shipped; verdict deferred' (clarity)
- cmd-audit.test.ts: added --base= empty-value + --base "" two-token-empty-string parser tests for symmetry with --baseline coverage

Author: SutuSebastian

.agents/rules/codemap.md

@@ -53,7 +53,7 @@ Validation: SQL is rejected at load time if it starts with DML/DDL (DELETE/DROP/
 
 **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.
 
-**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 B.6 baselines (`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).
+**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).
 
 **Targeted reads (`show` / `snippet`)**: precise lookup by exact symbol name without composing SQL. `show` returns metadata (`file_path:line_start-line_end` + `signature`); `snippet` returns the source text from disk plus `stale` / `missing` flags. Both share the same flag set (`--kind <k>` to filter by `symbols.kind`, `--in <path>` for file-scope filter — directory prefix or exact file). Output envelope is `{matches, disambiguation?}` — single match → `{matches: [{...}]}`; multi-match adds `disambiguation: {n, by_kind, files, hint}` so agents narrow without re-scanning. Name match is exact / case-sensitive — for fuzzy use `query` with `LIKE '%name%'`. Snippet stale-file behavior: `source` is always returned when the file exists; `stale: true` means the line range may have shifted (re-index with `bun src/index.ts` or `--files <path>` before acting on the source).
 

.agents/skills/codemap/SKILL.md

@@ -65,7 +65,7 @@ Each emitted delta carries its own `base` metadata so mixed-baseline audits are
 - **`query`** — one SQL statement. Args: `{sql, summary?, changed_since?, group_by?, format?}`. Same envelope as `codemap query --json`. Pass `format: "sarif"` or `"annotations"` to receive a formatted text payload (SARIF 2.1.0 doc / `::notice` lines); ad-hoc SQL gets `rule.id = codemap.adhoc`. Format is incompatible with `summary` / `group_by` (parser rejects with a structured `{error}`).
 - **`query_batch`** — MCP-only, no CLI counterpart. Args: `{statements: (string | {sql, summary?, changed_since?, group_by?})[], summary?, changed_since?, group_by?}`. Items are bare SQL strings (inherit batch-wide flag defaults) or objects (override on a per-key basis). Output is N-element array; per-element shape mirrors single-`query`'s output for that statement's effective flag set. Per-statement errors are isolated — failed statements return `{error}` in their slot; siblings still execute. SQL-only (no `recipe` polymorphism in items). `format` deferred to v1.x — annotation/sarif on a heterogeneous batch is awkward; call `query` per recipe instead.
 - **`query_recipe`** — `{recipe, summary?, changed_since?, group_by?, format?}`. Resolves the recipe id to SQL + per-row actions, then executes like `query`. Unknown recipe id returns a structured `{error}` pointing at the `codemap://recipes` resource. With `format: "sarif"`, `rule.id = codemap.<recipe>`, `rule.shortDescription` = recipe description, `rule.fullDescription` = the recipe's `<id>.md` body.
-- **`audit`** — `{base?, baseline_prefix?, baselines?: {files?, dependencies?, deprecated?}, summary?, no_index?}`. Composes per-delta snapshots into the `{head, deltas}` envelope. Three mutually-exclusive top-level sources: `base: <ref>` (git committish — worktree+reindex against any committish; sha-keyed cache under `.codemap/audit-cache/`; sub-100ms second run; requires git, errors cleanly on non-git projects); `baseline_prefix: "<prefix>"` (auto-resolve `<prefix>-{files,dependencies,deprecated}` from `query_baselines`); `baselines: {<key>: <name>}` (per-delta override — composes orthogonally with both). Per-delta `base.source` is `"ref"` (with `base.ref` + `base.sha`) or `"baseline"` (with `base.name` + `base.sha`). Auto-runs incremental index unless `no_index: true`; watch-active sessions skip the prelude automatically.
+- **`audit`** — `{base?, baseline_prefix?, baselines?: {files?, dependencies?, deprecated?}, summary?, no_index?}`. Composes per-delta snapshots into the `{head, deltas}` envelope. Two **primary** sources are mutually exclusive: `base: <ref>` (git committish — worktree+reindex against any committish; sha-keyed cache under `.codemap/audit-cache/`; sub-100ms second run; requires git, errors cleanly on non-git projects) OR `baseline_prefix: "<prefix>"` (auto-resolve `<prefix>-{files,dependencies,deprecated}` from `query_baselines`). Plus optional **per-delta overrides** via `baselines: {<key>: <name>}` that compose with either primary source. Per-delta `base.source` is `"ref"` (with `base.ref` + `base.sha`) or `"baseline"` (with `base.name` + `base.sha`). Auto-runs incremental index unless `no_index: true`; watch-active sessions skip the prelude automatically.
 - **`save_baseline`** — polymorphic `{name, sql? | recipe?}` with runtime exclusivity check (mirrors the CLI's single `--save-baseline=<name>` verb). Pass exactly one of `sql` or `recipe`.
 - **`list_baselines`** — no args; returns the array `codemap query --baselines --json` would print.
 - **`drop_baseline`** — `{name}`. Returns `{dropped: <name>}` on success or `isError` if the name doesn't exist.