**Query wiring:** Ad-hoc and recipe CLI SQL runs through **`printQueryResult`** in **`src/application/index-engine.ts`**, which sets **`PRAGMA query_only = 1`** before execute (parity with **`queryRows`** / **`executeQuery`**). **`src/cli/cmd-query.ts`** (argv, `--recipe` / `-r` alias, **`--summary`**, **`--changed-since`**, **`--group-by`**, **`--save-baseline`** / **`--baseline`** / **`--baselines`** / **`--drop-baseline`**, **`--ci`** (aliases `--format sarif` + non-zero exit on findings + quiet)), **`src/application/query-recipes.ts`** (**`QUERY_RECIPES`** — recipe registry proxy over bundled + project-local recipes; optional **`actions: RecipeAction[]`** per recipe), **`src/cli/main.ts`** (**`--recipes-json`** / **`--print-sql`** exit before config/DB). With **`--json`**, errors use **`{"error":"…"}`** on stdout for SQL failures, DB open, and bootstrap (same shape); **`runQueryCmd`** sets **`process.exitCode`** instead of **`process.exit`**. Friendlier "no `.codemap/index.db`" — `no such table: <X>` and `no such column: <X>` errors are rewritten in **`enrichQueryError`** to point at `codemap` / `codemap --full`. **`--summary`** filters output only — the SQL still executes against the index; output collapses to `{"count": N}` (with `--json`) or `count: N`. **`--changed-since <ref>`** post-filters result rows by `path` / `file_path` / `from_path` / `to_path` / `resolved_path` against `git diff --name-only <ref>...HEAD ∪ git status --porcelain` (helper: **`src/git-changed.ts`** — `getFilesChangedSince`, `filterRowsByChangedFiles`, `PATH_COLUMNS`); rows with no recognised path column pass through. **`--group-by <mode>`** (`owner` | `directory` | `package`) routes through **`runGroupedQuery`** in `cmd-query.ts` and emits `{"group_by": "<mode>", "groups": [{key, count, rows}]}` (or `[{key, count}]` with `--summary`); helpers in **`src/group-by.ts`** (`groupRowsBy`, `firstDirectory`, `loadCodeowners`, `discoverWorkspaceRoots`, `makePackageBucketizer`, `codeownersGlobToRegex`). CODEOWNERS lookup is last-match-wins (GitHub semantics); workspace discovery reads `package.json` `workspaces` and `pnpm-workspace.yaml` `packages:`. **`--save-baseline[=<name>]`** snapshots the result to the **`query_baselines`** table inside `<state-dir>/index.db` (default `.codemap/index.db`; no parallel JSON files; survives `--full` / SCHEMA bumps because the table is intentionally absent from `dropAll()`); name defaults to `--recipe` id, ad-hoc SQL needs an explicit name. **`--baseline[=<name>]`** replays the SQL, fetches the saved row set, and emits `{baseline:{...}, current_row_count, added: [...], removed: [...]}` (or `{baseline:{...}, current_row_count, added: N, removed: N}` with `--summary`); identity is per-row multiset equality (canonical `JSON.stringify` keyed frequency map — duplicate rows are tracked, not collapsed). No fuzzy "changed" category in v1. **`--group-by` is mutually exclusive** with both `--save-baseline` and `--baseline` (different output shapes). **`--baselines`** (read-only list) and **`--drop-baseline <name>`** complete the surface; helpers in **`src/db.ts`** (`upsertQueryBaseline`, `getQueryBaseline`, `listQueryBaselines`, `deleteQueryBaseline`). **Per-row recipe `actions`** are appended only when the user runs **`--recipe <id>`** with **`--json`** AND the recipe defines an `actions` template — programmatic `cm.query(sql)` and ad-hoc CLI SQL never carry actions; under `--baseline`, actions attach to `added` rows only (the rows the agent should act on). The **`components-by-hooks`** recipe ranks by hook count with a **comma-based tally** on **`hooks_used`** (no SQLite JSON1). Shipped **`templates/agents/`** documents **`codemap query --json`** as the primary agent example ([README § CLI](../README.md#cli)).
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