docs: align architecture, benchmark, golden-queries with audit fixes

- architecture.md: component detection heuristic (JSX return or hook
  usage), statement cache on Node, closeDb readonly for query paths,
  incremental/--files accept previously-indexed custom extensions
- benchmark.md: fixture description reflects enriched minimal/
- golden-queries.md: note 13-scenario Tier A coverage across all tables

Author: SutuSebastian

docs/architecture.md

@@ -129,7 +129,7 @@ A local SQLite database (`.codemap.db`) indexes the project tree and stores stru
 
 ### `--files` (targeted reindex)
 
-When specific file paths are passed via `--files`, the indexer skips git diff, git status, and the full filesystem glob scan. It reads the set of already-indexed paths from the database (for import resolution), then only processes the listed files. Files that no longer exist on disk are automatically removed from the index via `ON DELETE CASCADE`.
+When specific file paths are passed via `--files`, the indexer skips git diff, git status, and the full filesystem glob scan. It reads the set of already-indexed paths from the database (for import resolution), then only processes the listed files. Files with non-standard extensions (e.g. custom `include` globs) are accepted and indexed as text; a warning is printed but they are not skipped. Files that no longer exist on disk are automatically removed from the index via `ON DELETE CASCADE`.
 
 ## Programmatic usage
 
@@ -208,7 +208,7 @@ All tables use `STRICT` mode. Tables marked with `WITHOUT ROWID` store data dire
 | is_default       | INTEGER    | 1 if default export          |
 | re_export_source | TEXT       | Source module if re-exported |
 
-### `components` — React components (detected by JSX return + PascalCase) (`STRICT`)
+### `components` — React components (detected by PascalCase + JSX return or hook usage) (`STRICT`)
 
 | Column            | Type       | Description                   |
 | ----------------- | ---------- | ----------------------------- |
@@ -286,7 +286,7 @@ Uses the Rust-based `oxc-parser` via NAPI bindings to parse TypeScript/TSX/JS/JS
 - **Symbols**: Functions, arrow functions, classes, interfaces, type aliases, enums — with reconstructed signatures
 - **Imports**: All `import` statements with specifiers, source paths, and type-only flags
 - **Exports**: Named exports, default exports, re-exports
-- **Components**: React components detected via PascalCase name + JSX return. Extracts props type and hooks used
+- **Components**: React components detected via PascalCase name + (JSX return **or** hook usage). A PascalCase function in `.tsx`/`.jsx` that neither returns JSX nor calls hooks is indexed only as a symbol, not a component. Extracts props type and hooks used
 - **Markers**: `TODO`, `FIXME`, `HACK`, `NOTE` comments with line numbers
 
 ### CSS — `css-parser.ts` (`lightningcss`)
@@ -327,9 +327,10 @@ The indexer uses git to detect changes since the last indexed commit:
 
 1. **Stores `last_indexed_commit`** (HEAD SHA) in the `meta` table after each run
 2. On next run, computes `git diff --name-only <last_commit>..HEAD` + `git status --porcelain`
-3. Only re-indexes changed files (SHA-256 content comparison), using DB-sourced `indexedPaths` for import resolution (skips full `collectFiles()` glob scan)
-4. Deleted files are removed via `ON DELETE CASCADE` — deleting from `files` cascades to all related tables
-5. Falls back to full rebuild if commit history is incompatible (e.g. force push, branch switch)
+3. Filters changed files to those with a known extension **or** already present in the `files` table (so custom-extension files indexed during `--full` are re-indexed on subsequent incremental runs)
+4. Only re-indexes changed files (SHA-256 content comparison), using DB-sourced `indexedPaths` for import resolution (skips full `collectFiles()` glob scan)
+5. Deleted files are removed via `ON DELETE CASCADE` — deleting from `files` cascades to all related tables
+6. Falls back to full rebuild if commit history is incompatible (e.g. force push, branch switch)
 
 ## File Artifacts
 
@@ -436,7 +437,7 @@ Until the first release, Codemap keeps **`SCHEMA_VERSION` at 1**; pull `--full`
 
 ### `bun:sqlite` API
 
-All DDL and PRAGMA statements use `Database.run()`. The `sqlite-db.ts` wrapper abstracts both Bun (`bun:sqlite`) and Node (`better-sqlite3`). On Bun, `Database.query()` caches compiled statements; on Node, `better-sqlite3` re-prepares on each call via the wrapper's `run()` method. Read queries use the wrapper's `.query().all()` or `.get()`. Bulk inserts use the generic `batchInsert<T>()` helper with multi-row `INSERT ... VALUES (...),(...),(...)` in batches of 100, pre-computed placeholders, and zero-copy index-bounds iteration.
+All DDL and PRAGMA statements use `Database.run()`. The `sqlite-db.ts` wrapper abstracts both Bun (`bun:sqlite`) and Node (`better-sqlite3`). On Bun, `Database.query()` caches compiled statements internally. On Node, the wrapper maintains a `Map<string, Statement>` cache so repeated `run()` and `query()` calls with the same SQL reuse a single prepared statement. Read queries use the wrapper's `.query().all()` or `.get()`. Bulk inserts use the generic `batchInsert<T>()` helper with multi-row `INSERT ... VALUES (...),(...),(...)` in batches of 100, pre-computed placeholders, and zero-copy index-bounds iteration.
 
 ### PRAGMAs (set on every `openDb()`)
 
@@ -457,6 +458,8 @@ All DDL and PRAGMA statements use `Database.run()`. The `sqlite-db.ts` wrapper a
 | `analysis_limit` | `400` | Caps rows sampled by `optimize` to keep it fast                    |
 | `optimize`       | —     | Gathers query planner statistics (`sqlite_stat1`) for better plans |
 
+Read-only query paths (`printQueryResult`, `queryRows`) call `closeDb` with `{ readonly: true }`, which skips both PRAGMAs to avoid write contention under concurrent `codemap query` processes.
+
 ### WITHOUT ROWID tables
 
 Tables with a TEXT PRIMARY KEY and no auto-increment benefit from `WITHOUT ROWID` — the data is stored directly in the primary key B-tree instead of a separate rowid B-tree, eliminating a lookup indirection:

docs/benchmark.md

@@ -206,9 +206,12 @@ The benchmark also measures the cost of keeping the index fresh (3 runs each, sa
 
 #### `fixtures/minimal/`
 
-Small **private** package (not published) with intentional:
+Small **private** package (not published) with intentional coverage of all indexed tables:
 
-- `usePermissions`, `~/api/client` import, `components/shop/*`, `utils/date`, CSS variables, and a TODO marker.
+- **Symbols / imports / dependencies**: `usePermissions`, `~/api/client` path alias, `components/shop/*`, `utils/date`
+- **Components**: `ShopButton` (JSX return) + `FormatPrice` (PascalCase non-component — validates detection heuristic)
+- **CSS**: variables (`--color-brand`, `--spacing-md`), class selectors (`.container`, `.primary` in a `.module.css`), `@keyframes fadeIn`, `@import` edge
+- **Markers**: `TODO` (in `notes.md`) + `FIXME` (in `consumer.ts`)
 
 **Local:**
 

docs/golden-queries.md

@@ -69,12 +69,13 @@ Scenarios live in **`fixtures/golden/scenarios.json`** (Tier A) or optional **`s
 
 ## Status
 
-| Area                          | State                                                                   |
-| ----------------------------- | ----------------------------------------------------------------------- |
-| Tier A runner + CI            | **`bun run test:golden`** in `check`                                    |
-| Tier B external + schema      | **`test:golden:external`**, Zod in **`scripts/query-golden/schema.ts`** |
-| Subset matchers + budgets     | **`match`**, **`budgetMs`**, **`--strict-budget`**                      |
-| Optional CI for public corpus | Deferred — [roadmap § Backlog](./roadmap.md#backlog)                    |
+| Area                          | State                                                                                                                                   |
+| ----------------------------- | --------------------------------------------------------------------------------------------------------------------------------------- |
+| Tier A runner + CI            | **`bun run test:golden`** in `check`                                                                                                    |
+| Tier A scenario coverage      | 13 scenarios across all indexed tables: files, symbols, imports, exports, components, dependencies, markers, CSS vars/classes/keyframes |
+| Tier B external + schema      | **`test:golden:external`**, Zod in **`scripts/query-golden/schema.ts`**                                                                 |
+| Subset matchers + budgets     | **`match`**, **`budgetMs`**, **`--strict-budget`**                                                                                      |
+| Optional CI for public corpus | Deferred — [roadmap § Backlog](./roadmap.md#backlog)                                                                                    |
 
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