Reset dir singletons at file boundaries in isolate:false projects

[dev-milos]

mcp-meta-policy.test.ts fails intermittently on CI with a real mkdir under /memfs/... (EACCES/ENOENT), while passing on the dev box.

Cause: under isolate: false (v2-core, v2-integration) files in a worker fork share one module graph, so bobbit-dir's project root and the agent-dir runtime state are shared. docker-args.test.ts sets the root to a memfs fixture path and never restores it, so a later file that relies on the default resolves bobbitStateDir() under the leaked root. Which file loses depends on worker sharding, so it moved between the dev box and CI, and retry: 3 can't mask it — the retry reruns in the same fork.

Fix: a custom runner resets the project root and agent-dir state in onCollectStart, the one hook that runs per file before its module loads. beforeAll in a setup file fires once per worker, and beforeEach fires after the file's own beforeAll, so neither works. process.env is left alone — the fork-scoped gateway owns BOBBIT_*.

Deterministic repro (fails on master, passes here):

VITEST_MAX_WORKERS=1 vitest run --project v2-core \
  tests2/core/docker-args.test.ts tests2/core/mcp-meta-policy.test.ts

Full test:unit green at 2 and 3 workers (965 files); no test files or production code changed.

[greptile-apps]

Greptile Summary

Adds a custom per-file Vitest runner that resets shared directory state before collecting tests, and enables it for the non-isolated core and integration projects.

Confidence Score: 5/5

The PR appears safe to merge, with the reset scoped to the two non-isolated Vitest projects that share directory singleton state.

The runner restores both implicated in-memory directory states at each file boundary, while projects using module isolation do not require the custom runner.

Important Files Changed

Filename	Overview
tests2/harness/file-boundary-runner.ts	Introduces a per-file collection hook that restores the project-root and agent-directory singletons before each non-isolated test file loads.
vitest.config.ts	Configures the runner for the two projects that inherit isolate:false while leaving isolated projects unchanged.

Sequence Diagram

sequenceDiagram
  participant V as Vitest worker
  participant R as FileBoundaryRunner
  participant D as Directory singletons
  participant T as Test file
  V->>R: onCollectStart(file)
  R->>D: setProjectRoot(BASELINE_CWD)
  R->>D: resetAgentDirStateForTests()
  R->>V: super.onCollectStart(file)
  V->>T: collect and execute file

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