fix(apply): utilization hygiene — marker recipe, docs, tests

Fix replace-marker-kind SQL (drop content LIKE filter) and golden row.
Sync rename-preview recipe docs, MCP 18-tool count, synthesis shipped status,
apply_rows in agent-content, config example allowlist, allowlist unit tests,
and migrate-import-source CLI dry-run E2E. Add substrate-apply-utilization plan.

Author: SutuSebastian

README.md

@@ -221,7 +221,7 @@ codemap skill                                                   # full codemap S
 codemap rule                                                    # full codemap rule markdown to stdout
 
 # MCP server (Model Context Protocol) — for agent hosts (Claude Code, Cursor, Codex, generic MCP clients)
-codemap mcp                                                     # JSON-RPC on stdio (17 tools; watcher default-ON)
+codemap mcp                                                     # JSON-RPC on stdio (18 tools; watcher default-ON)
 # Tools (17): query, query_batch, query_recipe, audit, save_baseline,
 #        list_baselines, drop_baseline, context, validate, show, snippet, impact,
 #        affected, trace, explore, node, apply

codemap.config.example.json

@@ -4,6 +4,13 @@
   "synthesis": {
     "heuristicCalls": false
   },
+  "apply": {
+    "autoApplyRecipes": [
+      "migrate-import-source",
+      "replace-marker-kind",
+      "rename-preview"
+    ]
+  },
   "boundaries": [
     {
       "name": "ui-cant-touch-server",

docs/glossary.md

@@ -353,7 +353,7 @@ Rust-based CSS parser (NAPI bindings). Codemap's `src/css-parser.ts` uses its vi
 
 ### `codemap mcp` / MCP server
 
-Stdio MCP (Model Context Protocol) server exposing codemap's structural-query surface to agent hosts (Claude Code, Cursor, Codex, generic MCP clients) as JSON-RPC tools — eliminates the bash round-trip on every agent invocation. **17 tools:** `query`, `query_batch`, `query_recipe`, `audit`, `save_baseline`, `list_baselines`, `drop_baseline`, `context`, `validate`, `show`, `snippet`, `impact`, `affected`, `trace`, `explore`, `node`, `apply`. Each has a CLI twin with the same JSON payload except transport-only MCP resources (`codemap://mcp-instructions`, initialize `instructions`). Subset via **`CODEMAP_MCP_TOOLS`** ([agents.md § MCP tool allowlist](./agents.md#mcp-tool-allowlist)). **Resources:** `codemap://schema`, `codemap://skill`, `codemap://rule`, `codemap://mcp-instructions`, `codemap://recipes`, `codemap://recipes/{id}`, `codemap://files/{path}`, `codemap://symbols/{name}`. Resource freshness is split by contract: schema / skill / rule / mcp-instructions are lazy-cached per server process; recipes, files, and symbols are live read-per-call so inline recency fields and index mutations under `--watch` don't freeze at first read. HTTP's `GET /resources/{encoded-uri}` uses the same resource handler. **Baseline tools** (`save_baseline`, `list_baselines`, `drop_baseline`) mirror `query --save-baseline` / `--baselines` / `--drop-baseline`. **CLI twins:** `query batch`, `trace`, `explore`, `node`, `file`, `schema`, `symbols`, `context --include-snippets`. Tool input/output keys are snake_case on MCP/HTTP — Codemap's convention; CLI stays kebab. Output shape matches each tool's CLI JSON payload; MCP wraps payloads in `{content: [{type: "text", text: …}]}`. Bootstrap once at server boot; tool handlers (in `application/tool-handlers.ts`) and resource handlers (in `application/resource-handlers.ts`) are pure transport-agnostic — the same handlers serve `codemap serve` (HTTP) via `POST /tool/{name}` and `GET /resources/{encoded-uri}`. **Session lifecycle:** exits on client disconnect (stdin EOF, stdout broken pipe, parent process exit, SIGINT/SIGTERM) via `session-lifecycle.ts`; **no idle timeout** — the process stays up while the pipe is open even without tool calls (see [§ Session lifecycle](./architecture.md#cli-usage)). With `--watch`, the watcher starts before connect and drains on exit. Implementation: `src/cli/cmd-mcp.ts` (CLI shell) + `src/application/mcp-server.ts` (engine). See [`architecture.md` § MCP wiring](./architecture.md#cli-usage).
+Stdio MCP (Model Context Protocol) server exposing codemap's structural-query surface to agent hosts (Claude Code, Cursor, Codex, generic MCP clients) as JSON-RPC tools — eliminates the bash round-trip on every agent invocation. **18 tools:** `query`, `query_batch`, `query_recipe`, `audit`, `save_baseline`, `list_baselines`, `drop_baseline`, `context`, `validate`, `show`, `snippet`, `impact`, `affected`, `trace`, `explore`, `node`, `apply`, `apply_rows`. Each has a CLI twin with the same JSON payload except transport-only MCP resources (`codemap://mcp-instructions`, initialize `instructions`). Subset via **`CODEMAP_MCP_TOOLS`** ([agents.md § MCP tool allowlist](./agents.md#mcp-tool-allowlist)). **Resources:** `codemap://schema`, `codemap://skill`, `codemap://rule`, `codemap://mcp-instructions`, `codemap://recipes`, `codemap://recipes/{id}`, `codemap://files/{path}`, `codemap://symbols/{name}`. Resource freshness is split by contract: schema / skill / rule / mcp-instructions are lazy-cached per server process; recipes, files, and symbols are live read-per-call so inline recency fields and index mutations under `--watch` don't freeze at first read. HTTP's `GET /resources/{encoded-uri}` uses the same resource handler. **Baseline tools** (`save_baseline`, `list_baselines`, `drop_baseline`) mirror `query --save-baseline` / `--baselines` / `--drop-baseline`. **CLI twins:** `query batch`, `trace`, `explore`, `node`, `file`, `schema`, `symbols`, `context --include-snippets`. Tool input/output keys are snake_case on MCP/HTTP — Codemap's convention; CLI stays kebab. Output shape matches each tool's CLI JSON payload; MCP wraps payloads in `{content: [{type: "text", text: …}]}`. Bootstrap once at server boot; tool handlers (in `application/tool-handlers.ts`) and resource handlers (in `application/resource-handlers.ts`) are pure transport-agnostic — the same handlers serve `codemap serve` (HTTP) via `POST /tool/{name}` and `GET /resources/{encoded-uri}`. **Session lifecycle:** exits on client disconnect (stdin EOF, stdout broken pipe, parent process exit, SIGINT/SIGTERM) via `session-lifecycle.ts`; **no idle timeout** — the process stays up while the pipe is open even without tool calls (see [§ Session lifecycle](./architecture.md#cli-usage)). With `--watch`, the watcher starts before connect and drains on exit. Implementation: `src/cli/cmd-mcp.ts` (CLI shell) + `src/application/mcp-server.ts` (engine). See [`architecture.md` § MCP wiring](./architecture.md#cli-usage).
 
 ### `query_batch`