feat(checkpoints): v2 single-store rewrite with real pruning + disk guardrails (#20709)

Replaces the per-directory shadow-repo design with a single shared shadow
git store at ~/.hermes/checkpoints/store/. Object DB is now deduplicated
across every working directory the agent has ever touched; a dozen
worktrees of the same project cost near-zero in additional disk.

Why
---
Pre-v2 design had three compounding problems that let ~/.hermes/checkpoints/
grow to multi-GB on active machines:

1. Each working directory got its own full shadow git repo — no object
   dedup across projects or across worktrees of the same project.
2. _prune() was a documented no-op: max_snapshots only limited the
   /rollback listing. Loose objects accumulated forever.
3. Defaults: enabled=True, auto_prune=False — users paid the disk cost
   without ever asking for /rollback.

Field report on a single workstation: 847 MB across 47 shadow repos,
mostly redundant clones of the hermes-agent source tree.

Changes
-------
- tools/checkpoint_manager.py: full rewrite. Single bare store, per-project
  refs (refs/hermes/<hash>), per-project indexes (store/indexes/<hash>),
  per-project metadata (store/projects/<hash>.json with workdir +
  created_at + last_touch). On first v2 init, any pre-v2 per-directory
  shadow repos are auto-migrated into legacy-<timestamp>/ so the new
  store starts clean. _prune() now actually rewrites the per-project ref
  to the last max_snapshots commits and runs git gc --prune=now. New
  _enforce_size_cap() drops oldest commits round-robin across projects
  when the store exceeds max_total_size_mb. _drop_oversize_from_index()
  filters any single file larger than max_file_size_mb out of the snapshot.
- hermes_cli/checkpoints.py: new 'hermes checkpoints' CLI
  (status / list / prune / clear / clear-legacy) for managing the store
  outside a session.
- hermes_cli/config.py: flipped defaults — enabled=False, max_snapshots=20,
  auto_prune=True. Added max_total_size_mb=500, max_file_size_mb=10.
  Tightened DEFAULT_EXCLUDES (added target/, *.so/*.dylib/*.dll,
  *.mp4/*.mov, *.zip/*.tar.gz, .worktrees/, .mypy_cache/, etc.).
- run_agent.py / cli.py / gateway/run.py: thread the new kwargs through
  AIAgent and the startup auto_prune hooks.
- Tests rewritten to match v2 storage while keeping backwards-compat
  coverage for the pre-v2 prune path (per-directory shadow repos under
  base/ are still swept correctly for anyone mid-migration).
- Docs updated: user-guide/checkpoints-and-rollback.md explains the
  shared store, new defaults, migration, and the new CLI;
  reference/cli-commands.md documents 'hermes checkpoints'.

E2E validated
-------------
- Legacy migration: pre-v2 shadow repos auto-archived into legacy-<ts>/.
- Object dedup: two projects with an identical shared.py blob resolve to
  7 total objects in the store (v1 would have stored the blob twice).
- max_snapshots=3 actually enforced: after 6 commits, list shows 3.
- Orphan prune: deleting a project's workdir + 'hermes checkpoints prune
  --retention-days 0' removes its ref, index, and metadata; GC reclaims
  the objects.
- max_file_size_mb=1 excludes a 2 MB weights.bin while keeping the
  tracked source code files.
- hermes checkpoints {status,prune,clear,clear-legacy} all work from the
  CLI without an agent running.

Breaking / migration
--------------------
No in-place data migration — legacy per-directory shadow repos are moved
into legacy-<timestamp>/ on first run. Old /rollback history is still
accessible by inspecting the archive with git; run
'hermes checkpoints clear-legacy' to reclaim the space when ready. Users
relying on /rollback must now set checkpoints.enabled=true (or pass
--checkpoints) explicitly.

hermes_cli/config.py

@@ -574,21 +574,39 @@ DEFAULT_CONFIG = {
     },
 
     # Filesystem checkpoints — automatic snapshots before destructive file ops.
-    # When enabled, the agent takes a snapshot of the working directory once per
-    # conversation turn (on first write_file/patch call).  Use /rollback to restore.
+    # When enabled, the agent takes a snapshot of the working directory once
+    # per conversation turn (on first write_file/patch call).  Use /rollback
+    # to restore.
+    #
+    # Defaults changed in v2 (single shared shadow store, real pruning):
+    #   - enabled: True -> False   (opt-in; most users never use /rollback)
+    #   - max_snapshots: 50 -> 20  (now actually enforced via ref rewrite)
+    #   - auto_prune:   False -> True (orphans/stale pruned automatically)
+    # Opt in via ``hermes chat --checkpoints`` or set enabled=True here.
     "checkpoints": {
-        "enabled": True,
-        "max_snapshots": 50,  # Max checkpoints to keep per directory
-        # Auto-maintenance: shadow repos accumulate forever under
-        # ~/.hermes/checkpoints/ (one per cd'd working directory). Field
-        # reports put the typical offender at 1000+ repos / ~12 GB. When
-        # auto_prune is on, hermes sweeps at startup (at most once per
-        # min_interval_hours) and deletes:
-        #   * orphan repos: HERMES_WORKDIR no longer exists on disk
-        #   * stale repos:  newest mtime older than retention_days
-        # Opt-in so users who rely on /rollback against long-ago sessions
-        # never lose data silently.
-        "auto_prune": False,
+        "enabled": False,
+        # Max checkpoints to keep per working directory.  Pre-v2 this only
+        # limited the `/rollback` listing; v2 actually rewrites the ref and
+        # garbage-collects older commits.
+        "max_snapshots": 20,
+        # Hard ceiling on total ``~/.hermes/checkpoints/`` size (MB).  When
+        # exceeded, the oldest checkpoint per project is dropped in a
+        # round-robin pass until total size falls under the cap.
+        # 0 disables the size cap.
+        "max_total_size_mb": 500,
+        # Skip any single file larger than this when staging a checkpoint.
+        # Prevents accidental snapshotting of datasets, model weights, and
+        # other large generated assets.  0 disables the filter.
+        "max_file_size_mb": 10,
+        # Auto-maintenance: hermes sweeps the checkpoint base at startup
+        # (at most once per ``min_interval_hours``) and:
+        #   * deletes project entries whose workdir no longer exists (orphan)
+        #   * deletes project entries whose last_touch is older than
+        #     ``retention_days``
+        #   * GCs the single shared store to reclaim unreachable objects
+        #   * enforces ``max_total_size_mb`` across remaining projects
+        #   * deletes ``legacy-*`` archives older than ``retention_days``
+        "auto_prune": True,
         "retention_days": 7,
         "delete_orphans": True,
         "min_interval_hours": 24,