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.

cli.py

@@ -987,6 +987,7 @@ def _run_checkpoint_auto_maintenance() -> None:
             retention_days=int(cfg.get("retention_days", 7)),
             min_interval_hours=int(cfg.get("min_interval_hours", 24)),
             delete_orphans=bool(cfg.get("delete_orphans", True)),
+            max_total_size_mb=int(cfg.get("max_total_size_mb", 500)),
         )
     except Exception as exc:
         logger.debug("checkpoint auto-maintenance skipped: %s", exc)
@@ -2273,7 +2274,9 @@ class HermesCLI:
         if isinstance(cp_cfg, bool):
             cp_cfg = {"enabled": cp_cfg}
         self.checkpoints_enabled = checkpoints or cp_cfg.get("enabled", False)
-        self.checkpoint_max_snapshots = cp_cfg.get("max_snapshots", 50)
+        self.checkpoint_max_snapshots = cp_cfg.get("max_snapshots", 20)
+        self.checkpoint_max_total_size_mb = cp_cfg.get("max_total_size_mb", 500)
+        self.checkpoint_max_file_size_mb = cp_cfg.get("max_file_size_mb", 10)
         self.pass_session_id = pass_session_id
         # --ignore-rules: honor either the constructor flag or the env var set
         # by `hermes chat --ignore-rules` in hermes_cli/main.py. When true we
@@ -3845,6 +3848,8 @@ class HermesCLI:
                 thinking_callback=self._on_thinking,
                 checkpoints_enabled=self.checkpoints_enabled,
                 checkpoint_max_snapshots=self.checkpoint_max_snapshots,
+                checkpoint_max_total_size_mb=self.checkpoint_max_total_size_mb,
+                checkpoint_max_file_size_mb=self.checkpoint_max_file_size_mb,
                 pass_session_id=self.pass_session_id,
                 skip_context_files=self.ignore_rules,
                 skip_memory=self.ignore_rules,