fix: wire worktree flag into hermes CLI entry point + docs + tests

Critical fixes:
- Add --worktree/-w to hermes_cli/main.py argparse (both chat
  subcommand and top-level parser) so 'hermes -w' works via the
  actual CLI entry point, not just 'python cli.py -w'
- Pass worktree flag through cmd_chat() kwargs to cli_main()
- Handle worktree attr in bare 'hermes' and --resume/--continue paths

Bug fixes in cli.py:
- Skip worktree creation for --list-tools/--list-toolsets (wasteful)
- Wrap git worktree subprocess.run in try/except (crash on timeout)
- Add stale worktree pruning on startup (_prune_stale_worktrees):
  removes clean worktrees older than 24h left by crashed/killed sessions

Documentation updates:
- AGENTS.md: add --worktree to CLI commands table
- cli-config.yaml.example: add worktree config section
- website/docs/reference/cli-commands.md: add to core commands
- website/docs/user-guide/cli.md: add usage examples
- website/docs/user-guide/configuration.md: add config docs

Test improvements (17 → 31 tests):
- Stale worktree pruning (prune old clean, keep recent, keep dirty)
- Directory symlink via .worktreeinclude
- Edge cases (no commits, not a repo, pre-existing .worktrees/)
- CLI flag/config OR logic
- TERMINAL_CWD integration
- System prompt injection format

hermes_cli/main.py

@@ -167,6 +167,7 @@ def cmd_chat(args):
         "verbose": args.verbose,
         "query": args.query,
         "resume": getattr(args, "resume", None),
+        "worktree": getattr(args, "worktree", False),
     }
     # Filter out None values
     kwargs = {k: v for k, v in kwargs.items() if v is not None}
@@ -1217,6 +1218,7 @@ Examples:
     hermes config edit            Edit config in $EDITOR
     hermes config set model gpt-4 Set a config value
     hermes gateway                Run messaging gateway
+    hermes -w                     Start in isolated git worktree
     hermes gateway install        Install as system service
     hermes sessions list          List past sessions
     hermes update                 Update to latest version
@@ -1244,6 +1246,12 @@ For more help on a command:
         default=False,
         help="Resume the most recent CLI session"
     )
+    parser.add_argument(
+        "--worktree", "-w",
+        action="store_true",
+        default=False,
+        help="Run in an isolated git worktree (for parallel agents)"
+    )
     
     subparsers = parser.add_subparsers(dest="command", help="Command to run")
     
@@ -1290,6 +1298,12 @@ For more help on a command:
         default=False,
         help="Resume the most recent CLI session"
     )
+    chat_parser.add_argument(
+        "--worktree", "-w",
+        action="store_true",
+        default=False,
+        help="Run in an isolated git worktree (for parallel agents on the same repo)"
+    )
     chat_parser.set_defaults(func=cmd_chat)
 
     # =========================================================================
@@ -1850,6 +1864,8 @@ For more help on a command:
         args.provider = None
         args.toolsets = None
         args.verbose = False
+        if not hasattr(args, "worktree"):
+            args.worktree = False
         cmd_chat(args)
         return
     
@@ -1862,6 +1878,8 @@ For more help on a command:
         args.verbose = False
         args.resume = None
         args.continue_last = False
+        if not hasattr(args, "worktree"):
+            args.worktree = False
         cmd_chat(args)
         return