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

[SutuSebastian]

Summary

• Enforce one project root per process: initCodemap and configureResolver throw when switching roots mid-process; audit --base worktree reindex is exempt via runtime-swap.ts bracket in makeWorktreeReindex.
• Add maintainer test helpers (resetRuntimeForTest, installCodemapTestTeardown) with beforeEach/afterEach reset rolled out across initCodemap suites.
• Validate user config at loadUserConfig time (JSON + imported configs) and document the breaking tighten in api.ts / architecture.md.

Test plan

• bun test src/runtime.test.ts src/config.test.ts
• bun run check
• CI green
• CodeRabbit pass

Closes PR 3 of the security-hardening orchestrator program.

[coderabbitai]

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: ff7e0e14-347c-4cd1-918a-8178b473fe58

📥 Commits

Reviewing files that changed from the base of the PR and between aae172f and ea7e477.

📒 Files selected for processing (42)

• .changeset/runtime-test-isolation.md
• docs/architecture.md
• docs/plans/runtime-test-isolation.md
• docs/plans/security-hardening-orchestrator.md
• docs/roadmap.md
• scripts/agent-eval/parse-agent-log.test.ts
• src/api.test.ts
• src/api.ts
• src/application/affected-engine.test.ts
• src/application/audit-engine.test.ts
• src/application/audit-engine.ts
• src/application/boundary-rules.test.ts
• src/application/callback-synthesis-integration.test.ts
• src/application/churn-ingest.test.ts
• src/application/context-engine.test.ts
• src/application/get-changed-files.test.ts
• src/application/http-server.test.ts
• src/application/index-engine.test.ts
• src/application/index-freshness.test.ts
• src/application/ingest-coverage-run.test.ts
• src/application/mcp-server.test.ts
• src/application/output-budget.test.ts
• src/application/query-baseline.test.ts
• src/application/query-engine.test.ts
• src/application/query-recipes.test.ts
• src/application/recipe-recency.test.ts
• src/application/resource-handlers.test.ts
• src/application/run-call-resolve-synthesis.test.ts
• src/application/run-index.test.ts
• src/application/tool-handlers.test.ts
• src/application/trace-engine.test.ts
• src/cli/cmd-affected.test.ts
• src/cli/cmd-cli-parity-e2e.test.ts
• src/cli/cmd-validate.test.ts
• src/config.test.ts
• src/config.ts
• src/resolver.ts
• src/runtime-swap.ts
• src/runtime.test.ts
• src/runtime.ts
• src/test-helpers/runtime-reset.ts
• src/worker-pool.test.ts

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/runtime-test-isolation

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[changeset-bot]

🦋 Changeset detected

Latest commit: ea7e477

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 1 package

Name	Type
@stainless-code/codemap	Patch

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Click here if you're a maintainer who wants to add another changeset to this PR