fix(ingest): honor storage.git.auto_commit and memory.auto_commit

Both documented flags were read only for status display; every ingest path
squash-committed to main unconditionally, so setting either to false was a
silent no-op (the reported symptom: 'Memory ingest (external_ingest): ...'
commits despite memory.auto_commit: false).

Gate the commit at the squash-merge onto main — the one point where ingest work
becomes a permanent commit (intermediate session-worktree commits must still
happen for the squash to collapse). When auto-commit is off, apply the squash to
main's working tree and leave it staged instead of committing, so the run is
never silently discarded:

- GitService.stageSquashMergeIntoMain: shares the merge core with
  squashMergeIntoMain but stops before committing and returns the staged tree
  SHA (a valid diff/read ref).
- memory.auto_commit gates MemoryAgentService (its DB writes are eager, so the
  staged files stay consistent); the commit-message job is skipped.
- storage.git.auto_commit gates IngestBundleRunner; the wiki index is reconciled
  from the staged tree via the existing syncFromCommit (git diff/show accept a
  write-tree ref), and SL reindex already reads from files.

Config descriptions now state precisely what each flag gates and the staged
semantics when false.

packages/cli/test/context/memory/memory-agent.service.ingest.test.ts

@@ -40,6 +40,7 @@ interface BuiltMocks {
   slValidator: any;
   toolsetFactory: any;
   logger: any;
+  autoCommit: boolean;
 }
 
 const buildMocks = (overrides: Partial<BuiltMocks> = {}): BuiltMocks => {
@@ -111,6 +112,9 @@ const buildMocks = (overrides: Partial<BuiltMocks> = {}): BuiltMocks => {
     gitService: {
       revParseHead: vi.fn().mockResolvedValue('basesha'),
       squashMergeIntoMain: vi.fn().mockResolvedValue({ ok: true, squashSha: 'cafebabe', touchedPaths: ['a.yaml'] }),
+      stageSquashMergeIntoMain: vi
+        .fn()
+        .mockResolvedValue({ ok: true, touchedPaths: ['a.yaml'], stagedTree: 'deadbeeftree' }),
     },
     lockingService: {
       withLock: vi.fn().mockImplementation((_key: string, fn: () => Promise<unknown>) => fn()),
@@ -134,6 +138,7 @@ const buildMocks = (overrides: Partial<BuiltMocks> = {}): BuiltMocks => {
       }),
     },
     logger: { log: vi.fn(), warn: vi.fn(), error: vi.fn(), debug: vi.fn() },
+    autoCommit: true,
   };
 
   return { ...defaults, ...overrides };
@@ -151,6 +156,7 @@ const buildService = (mocks: BuiltMocks): MemoryAgentService =>
       llm: {
         memoryIngestionModel: mocks.appSettings.settings.llm.memoryIngestionModel,
       },
+      autoCommit: mocks.autoCommit,
     },
     promptService: mocks.prompt,
     skillsRegistry: mocks.skillsRegistry,
@@ -242,6 +248,26 @@ describe('MemoryAgentService.ingest — session-branch orchestration', () => {
     expect(result.commitHash).toBe('cafebabe');
   });
 
+  it('with auto_commit disabled, stages the session on main without committing or enqueuing a note', async () => {
+    const mocks = buildMocks({ autoCommit: false });
+    const svc = buildService(mocks);
+
+    const result = await svc.ingest(baseInput);
+
+    // Applied to main via the staging path, never the committing path.
+    expect(mocks.gitService.stageSquashMergeIntoMain).toHaveBeenCalledWith('session/chat-1');
+    expect(mocks.gitService.squashMergeIntoMain).not.toHaveBeenCalled();
+    // No commit means no commit-message enhancement job.
+    expect(mocks.configService.enqueueCommitMessageJobForExternalCommit).not.toHaveBeenCalled();
+    // The session still applied successfully; there is just no commit hash.
+    expect(result.commitHash).toBeNull();
+    expect(mocks.sessionWorktreeService.cleanup).toHaveBeenCalledWith(
+      expect.objectContaining({ chatId: 'chat-1' }),
+      'success',
+      expect.any(Object),
+    );
+  });
+
   it('normalizes load_skill output to markdown while preserving structured payload', async () => {
     const tempDir = await mkdtemp(join(tmpdir(), 'ktx-memory-skill-'));
     const skillDir = join(tempDir, 'memory_agent');

packages/cli/test/context/memory/memory-agent.service.test.ts

@@ -193,6 +193,7 @@ describe('MemoryAgentService.reconcileCrossRefs', () => {
         knowledge: { userScopedKnowledgeEnabled: false },
         slValidation: { probeRowCount: 1 },
         llm: { memoryIngestionModel: 'test-model' },
+        autoCommit: true,
       },
       promptService: undefined as never,
       skillsRegistry: undefined as never,
@@ -369,6 +370,7 @@ describe('MemoryAgentService.gateRevertInvalidSources (J3)', () => {
         knowledge: { userScopedKnowledgeEnabled: false },
         slValidation: { probeRowCount: 1 },
         llm: { memoryIngestionModel: 'test-model' },
+        autoCommit: true,
       },
       promptService: undefined as never,
       skillsRegistry: undefined as never,