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

website/docs/user-guide/configuration.md

@@ -407,6 +407,26 @@ memory:
   user_char_limit: 1375     # ~500 tokens
 ```
 
+## Git Worktree Isolation
+
+Enable isolated git worktrees for running multiple agents in parallel on the same repo:
+
+```yaml
+worktree: true    # Always create a worktree (same as hermes -w)
+# worktree: false # Default — only when -w flag is passed
+```
+
+When enabled, each CLI session creates a fresh worktree under `.worktrees/` with its own branch. Agents can edit files, commit, push, and create PRs without interfering with each other. Clean worktrees are removed on exit; dirty ones are kept for manual recovery.
+
+You can also list gitignored files to copy into worktrees via `.worktreeinclude` in your repo root:
+
+```
+# .worktreeinclude
+.env
+.venv/
+node_modules/
+```
+
 ## Context Compression
 
 ```yaml