chore: documentation updates and quick fixes

- Add missing command docs to SKILL.md (delegate, logs, status, doctor, notify, server, queue)
- Add KUGETSU_VERBOSITY to config options table
- Delete outdated test-kugetsu.sh (tests non-existent resume/stop commands)
- Fix Phase 3 status in kugetsu-architecture.md (was In Progress, now Implemented)
- Fix env rm quote handling (use grep -v instead of sed)
- Add error handling for opencode init command

skills/kugetsu/SKILL.md

@@ -48,6 +48,7 @@ A default config file is created during `kugetsu init` with commented examples:
 |----------|---------|-------------|
 | `MAX_CONCURRENT_AGENTS` | 3 | Maximum number of concurrent dev agents |
 | `KUGETSU_TEMP_DIR` | `~/.local/share/opencode/tool-output` | Temp directory for subagent tool output (useful in headless environments where /tmp is restricted) |
+| `KUGETSU_VERBOSITY` | `default` | PM agent verbosity level: `verbose`, `default`, or `quiet` |
 
 ### Environment Variables for Agents
 
@@ -255,6 +256,90 @@ kugetsu destroy --base -y
 
 **Note**: Destroying base also destroys PM agent since PM depends on base.
 
+### kugetsu delegate `<message>`
+
+Send a message to the PM agent for task coordination (fire-and-forget):
+```bash
+kugetsu delegate "work on issue #14"
+kugetsu delegate "review PR #92"
+```
+
+- Non-blocking: returns immediately, runs in background
+- PM agent processes the message asynchronously
+- Uses `KUGETSU_VERBOSITY` env var to control PM agent output verbosity
+- Log output stored in `~/.kugetsu/logs/delegate-<timestamp>.log`
+
+### kugetsu logs [n]
+
+Show recent delegation logs:
+```bash
+kugetsu logs           # Show last 10 logs
+kugetsu logs 20       # Show last 20 logs
+```
+
+- Logs are stored in `~/.kugetsu/logs/`
+- Automatically deletes logs older than 7 days
+
+### kugetsu status
+
+Check if kugetsu is properly initialized:
+```bash
+kugetsu status
+```
+
+Output:
+- `kugetsu_not_initialized` - No index file
+- `base_session_missing` - Base session not found
+- `pm_agent_missing` - PM agent not found
+- `ok` - Everything is initialized
+
+### kugetsu doctor [--fix]
+
+Diagnose and fix kugetsu issues:
+```bash
+kugetsu doctor              # Show diagnostic info
+kugetsu doctor --fix        # Attempt automatic repairs
+```
+
+- Checks index file existence
+- Validates base and PM agent sessions
+- With `--fix`: recreates PM agent if missing
+- With `--fix-permissions`: fixes session permissions in opencode database
+
+### kugetsu notify [list|clear]
+
+Show or clear notifications from PM agent:
+```bash
+kugetsu notify list         # Show unread notifications (default)
+kugetsu notify clear       # Mark all as read
+```
+
+- PM agent writes task completion notifications to `~/.kugetsu/notifications.json`
+- Shows timestamp, type, message, and issue ref for each notification
+
+### kugetsu server <list|add|remove|default|get>
+
+Manage git server configurations:
+```bash
+kugetsu server list              # List all configured servers
+kugetsu server add github https://github.com    # Add a server
+kugetsu server remove gitlab    # Remove a server
+kugetsu server default github   # Set default server
+kugetsu server get github       # Get server URL
+```
+
+### kugetsu queue <list|enqueue|dequeue|clear>
+
+Manage task queue for autonomous PM operation:
+```bash
+kugetsu queue list              # Show queued tasks
+kugetsu queue enqueue "task"   # Add task to queue
+kugetsu queue dequeue          # Remove next task from queue
+kugetsu queue clear            # Clear all queued tasks
+```
+
+- Queue stored in `~/.kugetsu/queue.json`
+
 ## Workflow Example
 
 ```bash