feat(runtime): guard root switches and isolate test global state

.changeset/runtime-test-isolation.md

@@ -0,0 +1,5 @@
+---
+"@stainless-code/codemap": patch
+---
+
+`createCodemap()` and the CLI now reject invalid project config at load time. A second `createCodemap()` with a different project root in the same process throws (audit `--base` worktree reindex is exempt).

docs/architecture.md

@@ -234,13 +234,13 @@ The npm package exports **`createCodemap`**, **`Codemap`** (`query`, `index`), *
 2. **`await cm.index({ mode, files?, quiet? })`** — same pipeline as the CLI (incremental / full / targeted).
 3. **`cm.query(sql)`** — read-only SQL against `.codemap/index.db` (opens the DB per call).
 
-**Constraint:** `initCodemap` is global to the process; only one active indexed project at a time.
+**Constraint:** One project root per process — a second `initCodemap` / `createCodemap` with a different `root` throws. Audit `--base` worktree reindex brackets temporary root swaps (internal swap guard). Re-init on the same root is allowed.
 
 ### User config
 
 Optional **`<state-dir>/config.{ts,js,json}`** (default `.codemap/config.*`; default export: object or async factory). **`--config <path>`** overrides with an explicit file (absolute or relative to cwd). Example shape: [`codemap.config.example.json`](../codemap.config.example.json). **Self-healing (D11):** `<state-dir>/.gitignore` is reconciled to canonical on every codemap boot via **`ensureStateGitignore`** (`src/application/state-dir.ts`); JSON config is reconciled via **`ensureStateConfig`** (`src/application/state-config.ts` — prunes unknown keys with a warning, sorts alphabetically, write-only-on-drift). TS/JS configs are validate-only at load time. Bumping the canonical `STATE_GITIGNORE_BODY` constant or the Zod schema IS the migration — every consumer's project repairs itself on next boot. Single attachment point: **`src/cli/bootstrap-codemap.ts`** runs the reconcilers before `loadUserConfig`.
 
-**Validation:** **`codemapUserConfigSchema`** ([Zod](https://zod.dev)) — strict object (unknown keys are rejected). **`defineConfig({ ... })`**, **`parseCodemapUserConfig`**, and **`resolveCodemapConfig`** (CLI and merged `createCodemap({ config })`) all go through the same schema. Invalid config throws **`TypeError`** with a short path/message list.
+**Validation:** **`codemapUserConfigSchema`** ([Zod](https://zod.dev)) — strict object (unknown keys are rejected). **`defineConfig({ ... })`**, **`parseCodemapUserConfig`**, and **`resolveCodemapConfig`** (CLI and merged `createCodemap({ config })`) all go through the same schema; **`createCodemap`** and the CLI load path validate config files at load time. Invalid config throws **`TypeError`** with a short path/message list.
 
 **Exports:** `codemapUserConfigSchema`, `parseCodemapUserConfig`, `defineConfig`, and **`CodemapUserConfig`** (inferred type) from the package entry — see **`src/config.ts`** / **`dist/index.d.mts`**.
 

docs/plans/security-hardening-orchestrator.md

@@ -21,11 +21,11 @@
 
 ## PR schedule
 
-| PR    | Plan                                                            | Status                                                                              | Blocks                              |
-| ----- | --------------------------------------------------------------- | ----------------------------------------------------------------------------------- | ----------------------------------- |
-| **1** | lifted → [`architecture.md`](../architecture.md) (plan retired) | **merged** ([#180](https://github.com/stainless-code/codemap/pull/180) · `a5caca8`) | —                                   |
-| **2** | lifted → [`architecture.md`](../architecture.md) (plan retired) | **PR open** (`fix/impact-inpath-homonyms`)                                          | —                                   |
-| **3** | [`runtime-test-isolation.md`](./runtime-test-isolation.md)      | **pending**                                                                         | PR **1** merged (PR **2** optional) |
+| PR    | Plan                                                            | Status                                                                                                  | Blocks |
+| ----- | --------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- | ------ |
+| **1** | lifted → [`architecture.md`](../architecture.md) (plan retired) | **merged** ([#180](https://github.com/stainless-code/codemap/pull/180) · `a5caca8`)                     | —      |
+| **2** | lifted → [`architecture.md`](../architecture.md) (plan retired) | **merged** ([#181](https://github.com/stainless-code/codemap/pull/181) · `aae172f`)                     | —      |
+| **3** | lifted → [`architecture.md`](../architecture.md) (plan retired) | **PR open** ([#182](https://github.com/stainless-code/codemap/pull/182) · `fix/runtime-test-isolation`) | —      |
 
 | — | — | **deferred** | golden `schema.test.ts` + path guards |
 | — | — | **skip** | atomic `ensureStateConfig` writes |
@@ -64,17 +64,18 @@ Evaluated 2026-06 against [roadmap § Floors](../roadmap.md#floors-v1-product-sh
 
 ## Session log
 
-| Date       | Event       | Notes                                                                        |
-| ---------- | ----------- | ---------------------------------------------------------------------------- |
-| 2026-06-10 | Triage      | ROI on 7 slices; 3-PR program adopted.                                       |
-| 2026-06-10 | PR 1 impl   | PR **1** committed on `fix/security-hardening-wave1`; harden pass in flight. |
-| 2026-06-05 | PR 1 harden | `/harden-pr full` — plan retired; contracts in architecture/glossary.        |
-| 2026-06-05 | PR 1 merge  | [#180](https://github.com/stainless-code/codemap/pull/180) → `a5caca8`.      |
-| 2026-06-05 | PR 2 start  | `fix/impact-inpath-homonyms` — `inPath` + homonym walks in impact-engine.    |
-| 2026-06-05 | PR 2 harden | `/harden-pr full` — plan retired; CLI/MCP/docs parity.                       |
-| —          | PR 2 merge  | _PR URL · merge SHA_                                                         |
-| —          | PR 3 start  | _from `main`_                                                                |
-| —          | PR 3 merge  | _fill · close orchestrator_                                                  |
+| Date       | Event       | Notes                                                                         |
+| ---------- | ----------- | ----------------------------------------------------------------------------- |
+| 2026-06-10 | Triage      | ROI on 7 slices; 3-PR program adopted.                                        |
+| 2026-06-10 | PR 1 impl   | PR **1** committed on `fix/security-hardening-wave1`; harden pass in flight.  |
+| 2026-06-05 | PR 1 harden | `/harden-pr full` — plan retired; contracts in architecture/glossary.         |
+| 2026-06-05 | PR 1 merge  | [#180](https://github.com/stainless-code/codemap/pull/180) → `a5caca8`.       |
+| 2026-06-05 | PR 2 start  | `fix/impact-inpath-homonyms` — `inPath` + homonym walks in impact-engine.     |
+| 2026-06-05 | PR 2 harden | `/harden-pr full` — plan retired; CLI/MCP/docs parity.                        |
+| 2026-06-05 | PR 2 merge  | [#181](https://github.com/stainless-code/codemap/pull/181) → `aae172f`.       |
+| 2026-06-05 | PR 3 start  | `fix/runtime-test-isolation` — root guards + test teardown + config validate. |
+| 2026-06-05 | PR 3 harden | `/harden-pr full` — plan retired; swap finally fix + API/config tests.        |
+| —          | PR 3 merge  | _fill · close orchestrator_                                                   |
 
 ---
 

docs/roadmap.md

@@ -108,7 +108,7 @@ Predicate-as-API only — enrich row shape and audit deltas; no standalone pass/
 - [ ] **`organize-imports` diff-shape recipe** — deterministic single-file import sort/group; `imports.line_number` + `source` substrate sufficient. Review-first (`auto_fixable: false`). Effort: S.
 - [ ] **`codemap-to-tsmorph` Path B adapter** — separate package experiment: `query_recipe` discovery → `ts-morph` / `jscodeshift` transforms for AST-shape edits codemap's substring executor defers (see [architecture § Rejected apply-path alternatives](./architecture.md#apply--input-modes-transport-and-policy)). Not an in-tree AST writer (Path A rejected). Effort: M.
 - [ ] **Apply write-safety hardening** — close apply TOCTOU: SHA-256 `hashContent` at phase-1 read, recheck disk hash immediately before phase-2 write (`file content changed` conflict); `fsync` temp file before `rename`; skip files with mixed CRLF/LF (`mixed line endings`). Preserves all-or-nothing on any conflict. Plan: [`plans/apply-write-safety.md`](./plans/apply-write-safety.md). Effort: L.
-- [ ] **Read-surface hardening (3 PRs)** — query/HTTP/validate safety, `impact` `inPath` homonyms, runtime guards + test teardown. **Orchestrator:** [`plans/security-hardening-orchestrator.md`](./plans/security-hardening-orchestrator.md). PR1 ([#180](https://github.com/stainless-code/codemap/pull/180), lifted to [architecture](./architecture.md)) · PR2 (`impact` homonyms, lifted to [architecture](./architecture.md)) · Plans: [PR3](./plans/runtime-test-isolation.md). Effort: S–M.
+- [ ] **Read-surface hardening (3 PRs)** — query/HTTP/validate safety, `impact` `inPath` homonyms, runtime guards + test teardown. **Orchestrator:** [`plans/security-hardening-orchestrator.md`](./plans/security-hardening-orchestrator.md). PR1 ([#180](https://github.com/stainless-code/codemap/pull/180), lifted to [architecture](./architecture.md)) · PR2 ([#181](https://github.com/stainless-code/codemap/pull/181), lifted to [architecture](./architecture.md)) · PR3 ([#182](https://github.com/stainless-code/codemap/pull/182), lifted to [architecture](./architecture.md)). Effort: S–M.
 - [ ] **`history` table** (deferred — revisit-triggered) — temporal queries: "when did symbol X get `@deprecated`?", "coverage trend over last 50 commits", "files that became dead this week". `audit --base <ref>` covers the most-common temporal question (PR-scoped diff) without schema growth, so the table earns its place only when bigger questions emerge. Two shapes (per-commit snapshots ~N × DB size; append-only event log heavier CTE walks); both pay an N-reindexes backfill cost (~30s per reindex). **Revisit triggers:** two consumers ship `jq`-based "audit-runs-over-time" workflows, OR `query_baselines` evolution becomes a recurring agent need.
 - [ ] **`codemap audit` verdict + thresholds** (v1.x) — `verdict: "pass" | "warn" | "fail"` driven by an `audit.deltas[<key>].{added_max, action}` field on the config object (`.codemap/config.{ts,js,json}`). Triggers: two consumers ship `jq`-based threshold scripts with similar shapes, OR one consumer asks with a concrete config sketch. Until then, raw deltas + consumer-side `jq` is the CI exit-code idiom. **Likely accelerant:** the Marketplace Action (next item) shipping is the most plausible path to firing the trigger — once `- uses: stainless-code/codemap@v1` is the dominant CI path, real `jq` threshold scripts will surface.
 - [ ] **GitHub Marketplace Action — publish + listing finish** — core Action implementation is in-tree: root `action.yml`, `query --ci`, `audit --format sarif` / `--ci`, package-manager detection, dogfood smoke, and opt-in `pr-comment` summary renderer have shipped. Remaining work is the release/listing slice: `MARKETPLACE.md`, `v1.0.0` / floating `v1` tags, Marketplace setup, sacrificial-repo smoke, and making `action-smoke` blocking once the Action tag exists. Action version stream is independent of CLI version (`package.json` currently drives CLI/npm version; Action publishes at its own `v1.0.0`). Plan: [`plans/github-marketplace-action.md`](./plans/github-marketplace-action.md). Effort: S.

scripts/agent-eval/parse-agent-log.test.ts

@@ -11,6 +11,7 @@ import { join } from "node:path";
 
 import { resolveCodemapConfig } from "../../src/config";
 import { initCodemap } from "../../src/runtime";
+import { installCodemapTestTeardown } from "../../src/test-helpers/runtime-reset";
 import { resolveGoldenQuery } from "../query-golden/resolve-golden-query";
 import { compareLogArms, summarizeLogComparison } from "./compare-live-logs";
 import { runLiveMcpArm } from "./live-mcp-arm";
@@ -43,6 +44,8 @@ import {
   traditionalToolSequence,
 } from "./traditional-probe";
 
+installCodemapTestTeardown();
+
 const sampleLog = join(
   import.meta.dir,
   "../../fixtures/agent-eval/sample-cursor-log.json",

src/api.test.ts

@@ -4,6 +4,9 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 
 import { createCodemap } from "./api";
+import { installCodemapTestTeardown } from "./test-helpers/runtime-reset";
+
+installCodemapTestTeardown();
 
 describe("createCodemap", () => {
   test("query runs against the index database", async () => {
@@ -13,4 +16,24 @@ describe("createCodemap", () => {
     const rows = cm.query("SELECT 1 as ok") as { ok: number }[];
     expect(rows[0]?.ok).toBe(1);
   });
+
+  test("throws when switching to a different root in the same process", async () => {
+    const rootA = mkdtempSync(join(tmpdir(), "codemap-api-a-"));
+    const rootB = mkdtempSync(join(tmpdir(), "codemap-api-b-"));
+    writeFileSync(join(rootA, "package.json"), "{}");
+    writeFileSync(join(rootB, "package.json"), "{}");
+    await createCodemap({ root: rootA });
+    await expect(createCodemap({ root: rootB })).rejects.toThrow(
+      /cannot switch project root/,
+    );
+  });
+
+  test("throws when config file is invalid at load", async () => {
+    const root = mkdtempSync(join(tmpdir(), "codemap-api-bad-"));
+    const configPath = join(root, "bad.json");
+    writeFileSync(configPath, JSON.stringify({ include: [1, 2] }));
+    await expect(
+      createCodemap({ root, configFile: configPath }),
+    ).rejects.toThrow(/include/);
+  });
 });

src/api.ts

@@ -45,7 +45,12 @@ export interface CodemapInitOptions {
  * and returns a {@link Codemap} handle.
  *
  * @remarks
- * Only one Codemap project per process: `initCodemap` is global; the last `createCodemap()` wins.
+ * One project root per process: a second `createCodemap()` with a different `root` throws.
+ * Re-initializing the same root is allowed. Audit `--base` worktree reindex is the only
+ * production path that may temporarily switch roots.
+ *
+ * Invalid project config (unknown keys, wrong types) throws at load time via the same
+ * schema as {@link parseCodemapUserConfig}.
  */
 export async function createCodemap(
   options: CodemapInitOptions = {},

src/application/affected-engine.test.ts

@@ -4,6 +4,10 @@ import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
+import { installCodemapTestTeardown } from "../test-helpers/runtime-reset";
+
+installCodemapTestTeardown();
+
 import { resolveCodemapConfig } from "../config";
 import { closeDb, createTables, openDb } from "../db";
 import { initCodemap } from "../runtime";