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.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,