feat: filesystem checkpoints and /rollback command

Automatic filesystem snapshots before destructive file operations,
with user-facing rollback.  Inspired by PR #559 (by @alireza78a).

Architecture:
- Shadow git repos at ~/.hermes/checkpoints/{hash}/ via GIT_DIR
- CheckpointManager: take/list/restore, turn-scoped dedup, pruning
- Transparent — the LLM never sees it, no tool schema, no tokens
- Once per turn — only first write_file/patch triggers a snapshot

Integration:
- Config: checkpoints.enabled + checkpoints.max_snapshots
- CLI flag: hermes --checkpoints
- Trigger: run_agent.py _execute_tool_calls() before write_file/patch
- /rollback slash command in CLI + gateway (list, restore by number)
- Pre-rollback snapshot auto-created on restore (undo the undo)

Safety:
- Never blocks file operations — all errors silently logged
- Skips root dir, home dir, dirs >50K files
- Disables gracefully when git not installed
- Shadow repo completely isolated from project git

Tests: 35 new tests, all passing (2798 total suite)
Docs: feature page, config reference, CLI commands reference

run_agent.py

@@ -185,6 +185,8 @@ class AIAgent:
         honcho_session_key: str = None,
         iteration_budget: "IterationBudget" = None,
         fallback_model: Dict[str, Any] = None,
+        checkpoints_enabled: bool = False,
+        checkpoint_max_snapshots: int = 50,
     ):
         """
         Initialize the AI Agent.
@@ -486,6 +488,13 @@ class AIAgent:
         # Cached system prompt -- built once per session, only rebuilt on compression
         self._cached_system_prompt: Optional[str] = None
         
+        # Filesystem checkpoint manager (transparent — not a tool)
+        from tools.checkpoint_manager import CheckpointManager
+        self._checkpoint_mgr = CheckpointManager(
+            enabled=checkpoints_enabled,
+            max_snapshots=checkpoint_max_snapshots,
+        )
+        
         # SQLite session store (optional -- provided by CLI or gateway)
         self._session_db = session_db
         if self._session_db:
@@ -2706,6 +2715,18 @@ class AIAgent:
                 except Exception as cb_err:
                     logging.debug(f"Tool progress callback error: {cb_err}")
 
+            # Checkpoint: snapshot working dir before file-mutating tools
+            if function_name in ("write_file", "patch") and self._checkpoint_mgr.enabled:
+                try:
+                    file_path = function_args.get("path", "")
+                    if file_path:
+                        work_dir = self._checkpoint_mgr.get_working_dir_for_path(file_path)
+                        self._checkpoint_mgr.ensure_checkpoint(
+                            work_dir, f"before {function_name}"
+                        )
+                except Exception:
+                    pass  # never block tool execution
+
             tool_start_time = time.time()
 
             if function_name == "todo":
@@ -3215,6 +3236,9 @@ class AIAgent:
         self.clear_interrupt()
         
         while api_call_count < self.max_iterations and self.iteration_budget.remaining > 0:
+            # Reset per-turn checkpoint dedup so each iteration can take one snapshot
+            self._checkpoint_mgr.new_turn()
+
             # Check for interrupt request (e.g., user sent new message)
             if self._interrupt_requested:
                 interrupted = True