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

cli-config.yaml.example

@@ -50,6 +50,16 @@ model:
 #   # Data policy: "allow" (default) or "deny" to exclude providers that may store data
 #   # data_collection: "deny"
 
+# =============================================================================
+# Git Worktree Isolation
+# =============================================================================
+# When enabled, each CLI session creates an isolated git worktree so multiple
+# agents can work on the same repo concurrently without file collisions.
+# Equivalent to always passing --worktree / -w on the command line.
+#
+# worktree: true    # Always create a worktree when in a git repo
+# worktree: false   # Default — only create when -w flag is passed
+
 # =============================================================================
 # Terminal Tool Configuration
 # =============================================================================