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/ingest/ingest-bundle.runner.isolated-diff.test.ts

@@ -199,6 +199,7 @@ function makeDeps(
     storage: {
       homeDir: join(runtime.configDir, '.ktx'),
       systemGitAuthor: { name: 'KTX Test', email: 'system@ktx.local' },
+      autoCommit: true,
       resolveUploadDir: (id) => join(runtime.homeDir, 'upload', id),
       resolvePullDir: (id) => join(runtime.homeDir, 'pull', id),
       resolveTranscriptDir: (id) => join(runtime.configDir, '.ktx/ingest-transcripts', id),