FN-6206: quarantine flaky engine tests

Move undocumented flaky engine tests into the formal quarantine path.

- add quarantine ledger entries for flaky engine test files observed under concurrent/full-suite load
- exclude the quarantined engine test files from vitest projects so they no longer run in gate and reliability pools
- remove the undocumented it.skip markers by quarantining at the file/config level instead

Files changed:
 .../__tests__/merger-file-scope-invariant.test.ts  |  4 ++--
 .../src/__tests__/project-engine-manager.test.ts   |  2 +-
 packages/engine/vitest.config.ts                   | 10 ++++++++--
 scripts/lib/test-quarantine.json                   | 23 +++++++++++++++++++++-
 4 files changed, 33 insertions(+), 6 deletions(-)

Fusion-Task-Id: FN-6206

Fusion-Task-Lineage: 8d88725e-1e92-4a06-aaa6-be34287e613a

packages/engine/src/__tests__/merger-file-scope-invariant.test.ts

@@ -157,7 +157,7 @@ describe("assertSquashOverlapsFileScope", () => {
   // (which reports staged files unrelated to the test scope and trips the
   // FileScopeViolationError). The same logic is covered by the existing
   // real-git fixture tests in reliability-interactions/workflow-and-file-scope.
-  it.skip("accepts declared scope as a single changeset file when staged matches exactly", async () => {
+  it("accepts declared scope as a single changeset file when staged matches exactly", async () => {
     const store = createInvariantStore([".changeset/fn-4767-pr-flow.md"]);
     mockStagedFiles([".changeset/fn-4767-pr-flow.md"]);
 
@@ -170,7 +170,7 @@ describe("assertSquashOverlapsFileScope", () => {
   });
 
   // Skipped: same flake mode as the test above.
-  it.skip("accepts declared scope as a changeset glob when staged file matches", async () => {
+  it("accepts declared scope as a changeset glob when staged file matches", async () => {
     const store = createInvariantStore([".changeset/*.md"]);
     mockStagedFiles([".changeset/fn-4767-pr-flow.md"]);
 

packages/engine/src/__tests__/project-engine-manager.test.ts

@@ -550,7 +550,7 @@ describe("ProjectEngineManager", () => {
     // Flake under full reliability-suite load: 30s timeout, but passes in ~46ms
     // standalone. Setinterval-driven reconciliation appears to race with vitest
     // fake-timer contention when other reliability-pool files are co-resident.
-    it.skip("retries failed project starts on subsequent reconciliation ticks", async () => {
+    it("retries failed project starts on subsequent reconciliation ticks", async () => {
       // Track how many times start() is called to fail only the FIRST set
       let startCallCount = 0;
       const manager = new ProjectEngineManager(centralCore);

packages/engine/vitest.config.ts

@@ -68,7 +68,6 @@ export default defineConfig({
             "src/__tests__/merger-post-merge.test.ts",
             "src/__tests__/merger-conflict-resolution.test.ts",
             "src/__tests__/merger-diff-scope.test.ts",
-            "src/__tests__/merger-file-scope-invariant.test.ts",
             "src/__tests__/merger-landed-files-capture.test.ts",
             "src/__tests__/branch-attribution.test.ts",
             "src/__tests__/executor-core.test.ts",
@@ -86,7 +85,11 @@ export default defineConfig({
             "src/__tests__/workflow-node-handlers.test.ts",
             "src/__tests__/workflow-policy-ownership-map.test.ts",
           ],
-          exclude: ["node_modules/**", "dist/**"],
+          exclude: [
+            "node_modules/**",
+            "dist/**",
+            "src/__tests__/merger-file-scope-invariant.test.ts",
+          ],
         },
       },
       {
@@ -102,6 +105,9 @@ export default defineConfig({
             "src/**/*.slow.test.ts",
             "node_modules/**",
             "dist/**",
+            "src/__tests__/merger-file-scope-invariant.test.ts",
+            "src/__tests__/project-engine-manager.test.ts",
+            "src/__tests__/merger-ai-cleanup.test.ts",
           ],
         },
       },

scripts/lib/test-quarantine.json

@@ -1,4 +1,25 @@
 {
   "$comment": "Flaky-test quarantine ledger (deletion ratchet — see AGENTS.md 'Flaky tests: quarantine on sight' and docs/testing.md 'Quarantine ledger and the deletion ratchet'). A test observed failing without a corresponding real bug is quarantined ON SIGHT: add an entry here AND a matching one-line `exclude` entry in that package's vitest config, in the same commit. Every entry needs a non-empty `reason` (link the failing run) and a `quarantinedAt` date — the entry expires 14 days later, at which point the test file is DELETED unless someone rescues it with evidence it catches real regressions plus a root-cause fix (never appeasement). There is deliberately no loader module and no automation around this file: it is a dated record, the vitest config exclude is the mechanism, and the sweep is policy executed by whoever touches the suite.",
-  "entries": []
+  "entries": [
+    {
+      "file": "packages/engine/src/__tests__/project-engine-manager.test.ts",
+      "reason": "Flake: setInterval-driven reconciliation races with vitest fake-timer contention under full reliability-suite load. Test passes standalone (~46ms) but times out (30s) when reliability-pool files are co-resident. FN-6206.",
+      "quarantinedAt": "2026-06-10"
+    },
+    {
+      "file": "packages/engine/src/__tests__/merger-file-scope-invariant.test.ts",
+      "reason": "Flake: vi.mock('node:child_process') occasionally doesn't take under workspace-concurrent runs, letting real git binary leak and report staged files unrelated to test scope (trips FileScopeViolationError). Same logic covered by real-git fixture tests in reliability-interactions/workflow-and-file-scope. FN-6206.",
+      "quarantinedAt": "2026-06-10"
+    },
+    {
+      "file": "packages/engine/src/__tests__/merger-file-scope-invariant.test.ts",
+      "reason": "Flake: same mock-contention mode as the sibling changeset-file test above (vi.mock('node:child_process') not taking under concurrent load). FN-6206.",
+      "quarantinedAt": "2026-06-10"
+    },
+    {
+      "file": "packages/engine/src/__tests__/merger-ai-cleanup.test.ts",
+      "reason": "Flake observed during FN-6206 verification: `pruneExistingAiMergeWorktrees skips active-session paths` failed in full `pnpm --filter @fusion/engine test` runs while the file passed standalone, indicating suite-order/concurrency sensitivity. Follow-up FN-6207.",
+      "quarantinedAt": "2026-06-10"
+    }
+  ]
 }