docs: terminology sweep - add missing terms and unify patrol templates

Missing terms added:
- Stranded Convoy: convoy with ready work but no polecats (convoy.md)
- Shiny Workflow: canonical polecat formula (molecules.md)
- Health Check Commands: gt deacon health-check/health-state (reference.md)
- MQ Commands: gt mq list/submit/retry/etc (reference.md)

Patrol template fixes:
- Unified wisp spawn commands to use bd mol wisp consistently
- Fixed Refinery incorrect bd mol spawn --wisp (command does not exist)
- Fixed Deacon status=pinned to status=hooked
- Standardized startup protocol header naming
- Added Working Directory section to Witness and Refinery templates

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/reference.md

@@ -545,6 +545,24 @@ gt stop --all                # Kill all sessions
 gt stop --rig <name>         # Kill rig sessions
 ```
 
+### Health Check
+
+```bash
+gt deacon health-check <agent>   # Send health check ping, track response
+gt deacon health-state           # Show health check state for all agents
+```
+
+### Merge Queue (MQ)
+
+```bash
+gt mq list [rig]             # Show the merge queue
+gt mq next [rig]             # Show highest-priority merge request
+gt mq submit                 # Submit current branch to merge queue
+gt mq status <id>            # Show detailed merge request status
+gt mq retry <id>             # Retry a failed merge request
+gt mq reject <id>            # Reject a merge request
+```
+
 ## Beads Commands (bd)
 
 ```bash