refactor: Update bd pour/wisp → bd mol pour/wisp

Beads CLI restructured: pour and wisp are now subcommands of mol.
- bd pour → bd mol pour
- bd wisp → bd mol wisp

Updated all documentation, templates, and code to use new command structure.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.beads/formulas/beads-release.formula.toml

@@ -14,7 +14,7 @@ This formula orchestrates a complete release cycle:
 ## Usage
 
 ```bash
-bd wisp create beads-release --var version=0.37.0
+bd mol wisp create beads-release --var version=0.37.0
 ```
 
 Or assign to a polecat:

.beads/formulas/mol-gastown-boot.formula.json

@@ -0,0 +1,62 @@
+{
+  "formula": "mol-gastown-boot",
+  "description": "Mayor bootstraps Gas Town via a verification-gated lifecycle molecule.\n\n## Purpose\nWhen Mayor executes \"boot up gas town\", this proto provides the workflow.\nEach step has action + verification - steps stay open until outcome is confirmed.\n\n## Key Principles\n1. **Verification-gated steps** - Not \"command ran\" but \"outcome confirmed\"\n2. **gt peek for verification** - Capture session output to detect stalls\n3. **gt nudge for recovery** - Reliable message delivery to unstick agents\n4. **Parallel where possible** - Witnesses and refineries can start in parallel\n5. **Ephemeral execution** - Boot is a wisp, squashed to digest after completion\n\n## Execution\n```bash\nbd mol wisp mol-gastown-boot  # Create wisp\n```",
+  "version": 1,
+  "steps": [
+    {
+      "id": "ensure-daemon",
+      "title": "Ensure daemon",
+      "description": "Verify the Gas Town daemon is running.\n\n## Action\n```bash\ngt daemon status || gt daemon start\n```\n\n## Verify\n1. Daemon PID file exists: `~/.gt/daemon.pid`\n2. Process is alive: `kill -0 $(cat ~/.gt/daemon.pid)`\n3. Daemon responds: `gt daemon status` returns success\n\n## OnFail\nCannot start daemon. Log error and continue - some commands work without daemon."
+    },
+    {
+      "id": "ensure-deacon",
+      "title": "Ensure deacon",
+      "needs": ["ensure-daemon"],
+      "description": "Start the Deacon and verify patrol mode is active.\n\n## Action\n```bash\ngt deacon start\n```\n\n## Verify\n1. Session exists: `tmux has-session -t gt-deacon 2>/dev/null`\n2. Not stalled: `gt peek deacon/` does NOT show \"> Try\" prompt\n3. Heartbeat fresh: `deacon/heartbeat.json` modified < 2 min ago\n\n## OnStall\n```bash\ngt nudge deacon/ \"Start patrol.\"\nsleep 30\n# Re-verify\n```"
+    },
+    {
+      "id": "ensure-witnesses",
+      "title": "Ensure witnesses",
+      "needs": ["ensure-deacon"],
+      "type": "parallel",
+      "description": "Parallel container: Start all rig witnesses.\n\nChildren execute in parallel. Container completes when all children complete.",
+      "children": [
+        {
+          "id": "ensure-gastown-witness",
+          "title": "Ensure gastown witness",
+          "description": "Start the gastown rig Witness.\n\n## Action\n```bash\ngt witness start gastown\n```\n\n## Verify\n1. Session exists: `tmux has-session -t gastown-witness 2>/dev/null`\n2. Not stalled: `gt peek gastown/witness` does NOT show \"> Try\" prompt\n3. Heartbeat fresh: Last patrol cycle < 5 min ago"
+        },
+        {
+          "id": "ensure-beads-witness",
+          "title": "Ensure beads witness",
+          "description": "Start the beads rig Witness.\n\n## Action\n```bash\ngt witness start beads\n```\n\n## Verify\n1. Session exists: `tmux has-session -t beads-witness 2>/dev/null`\n2. Not stalled: `gt peek beads/witness` does NOT show \"> Try\" prompt\n3. Heartbeat fresh: Last patrol cycle < 5 min ago"
+        }
+      ]
+    },
+    {
+      "id": "ensure-refineries",
+      "title": "Ensure refineries",
+      "needs": ["ensure-deacon"],
+      "type": "parallel",
+      "description": "Parallel container: Start all rig refineries.\n\nChildren execute in parallel. Container completes when all children complete.",
+      "children": [
+        {
+          "id": "ensure-gastown-refinery",
+          "title": "Ensure gastown refinery",
+          "description": "Start the gastown rig Refinery.\n\n## Action\n```bash\ngt refinery start gastown\n```\n\n## Verify\n1. Session exists: `tmux has-session -t gastown-refinery 2>/dev/null`\n2. Not stalled: `gt peek gastown/refinery` does NOT show \"> Try\" prompt\n3. Queue processing: Refinery can receive merge requests"
+        },
+        {
+          "id": "ensure-beads-refinery",
+          "title": "Ensure beads refinery",
+          "description": "Start the beads rig Refinery.\n\n## Action\n```bash\ngt refinery start beads\n```\n\n## Verify\n1. Session exists: `tmux has-session -t beads-refinery 2>/dev/null`\n2. Not stalled: `gt peek beads/refinery` does NOT show \"> Try\" prompt\n3. Queue processing: Refinery can receive merge requests"
+        }
+      ]
+    },
+    {
+      "id": "verify-town-health",
+      "title": "Verify town health",
+      "needs": ["ensure-witnesses", "ensure-refineries"],
+      "description": "Final verification that Gas Town is healthy.\n\n## Action\n```bash\ngt status\n```\n\n## Verify\n1. Daemon running: Shows daemon status OK\n2. Deacon active: Shows deacon in patrol mode\n3. All witnesses: Each rig witness shows active\n4. All refineries: Each rig refinery shows active\n\n## OnFail\nLog degraded state but consider boot complete. Some agents may need manual recovery.\nRun `gt doctor` for detailed diagnostics."
+    }
+  ]
+}

.beads/formulas/mol-gastown-boot.formula.toml

@@ -14,7 +14,7 @@ Each step has action + verification - steps stay open until outcome is confirmed
 
 ## Execution
 ```bash
-bd wisp mol-gastown-boot  # Create wisp
+bd mol wisp mol-gastown-boot  # Create wisp
 ```"""
 formula = "mol-gastown-boot"
 version = 1

README.md

@@ -98,7 +98,7 @@ needs = ["test"]
 ```bash
 bd formula list                    # See available formulas
 bd cook shiny                      # Cook into a protomolecule
-bd pour shiny --var feature=auth   # Create runnable molecule
+bd mol pour shiny --var feature=auth   # Create runnable molecule
 gt sling gt-xyz myproject          # Assign to worker
 ```
 

docs/reference.md

@@ -110,9 +110,9 @@ Formula (source TOML) ─── "Ice-9"
     ▼ bd cook
 Protomolecule (frozen template) ─── Solid
     │
-    ├─▶ bd pour ──▶ Mol (persistent) ─── Liquid ──▶ bd squash ──▶ Digest
+    ├─▶ bd mol pour ──▶ Mol (persistent) ─── Liquid ──▶ bd squash ──▶ Digest
     │
-    └─▶ bd wisp ──▶ Wisp (ephemeral) ─── Vapor ──┬▶ bd squash ──▶ Digest
+    └─▶ bd mol wisp ──▶ Wisp (ephemeral) ─── Vapor ──┬▶ bd squash ──▶ Digest
                                                   └▶ bd burn ──▶ (gone)
 ```
 
@@ -130,8 +130,8 @@ bd cook <formula>            # Formula → Proto
 # Molecules
 bd mol list                  # Available protos
 bd mol show <id>             # Proto details
-bd pour <proto>              # Create mol
+bd mol pour <proto>          # Create mol
-bd wisp <proto>              # Create wisp
+bd mol wisp <proto>          # Create wisp
 bd mol bond <proto> <parent> # Attach to existing mol
 bd mol squash <id>           # Condense to digest
 bd mol burn <id>             # Discard wisp
@@ -237,7 +237,7 @@ Deacon, Witness, and Refinery run continuous patrol loops using wisps:
 | **Refinery** | `mol-refinery-patrol` | Process merge queue, review PRs |
 
 ```
-1. bd wisp mol-<role>-patrol
+1. bd mol wisp mol-<role>-patrol
 2. Execute steps (check workers, process queue, run plugins)
 3. bd mol squash (or burn if routine)
 4. Loop

internal/cmd/prime.go

@@ -459,7 +459,7 @@ func outputStartupDirective(ctx RoleContext) {
 		fmt.Println("2. Check mail: `gt mail inbox` - look for 🤝 HANDOFF messages")
 		fmt.Println("3. Check for attached patrol: `gt mol status`")
 		fmt.Println("   - If mol attached → **RUN IT** (resume from current step)")
-		fmt.Println("   - If no mol → create patrol: `bd wisp mol-witness-patrol`")
+		fmt.Println("   - If no mol → create patrol: `bd mol wisp mol-witness-patrol`")
 	case RolePolecat:
 		fmt.Println()
 		fmt.Println("---")
@@ -480,7 +480,7 @@ func outputStartupDirective(ctx RoleContext) {
 		fmt.Println("2. Check mail: `gt mail inbox` - look for 🤝 HANDOFF messages")
 		fmt.Println("3. Check for attached patrol: `gt mol status`")
 		fmt.Println("   - If mol attached → **RUN IT** (resume from current step)")
-		fmt.Println("   - If no mol → create patrol: `bd wisp mol-refinery-patrol`")
+		fmt.Println("   - If no mol → create patrol: `bd mol wisp mol-refinery-patrol`")
 	case RoleCrew:
 		fmt.Println()
 		fmt.Println("---")
@@ -502,7 +502,7 @@ func outputStartupDirective(ctx RoleContext) {
 		fmt.Println("3. Check mail: `gt mail inbox` - look for 🤝 HANDOFF messages")
 		fmt.Println("4. Check for attached patrol: `gt mol status`")
 		fmt.Println("   - If mol attached → **RUN IT** (resume from current step)")
-		fmt.Println("   - If no mol → create patrol: `bd wisp mol-deacon-patrol`")
+		fmt.Println("   - If no mol → create patrol: `bd mol wisp mol-deacon-patrol`")
 	}
 }
 

internal/doctor/wisp_check.go

@@ -124,15 +124,15 @@ func (c *WispGCCheck) countAbandonedWisps(rigPath string) int {
 	return count
 }
 
-// Fix runs bd wisp gc in each rig with abandoned wisps.
+// Fix runs bd mol wisp gc in each rig with abandoned wisps.
 func (c *WispGCCheck) Fix(ctx *CheckContext) error {
 	var lastErr error
 
 	for rigName := range c.abandonedRigs {
 		rigPath := filepath.Join(ctx.TownRoot, rigName)
 
-		// Run bd --no-daemon wisp gc
+		// Run bd --no-daemon mol wisp gc
-		cmd := exec.Command("bd", "--no-daemon", "wisp", "gc")
+		cmd := exec.Command("bd", "--no-daemon", "mol", "wisp", "gc")
 		cmd.Dir = rigPath
 		if output, err := cmd.CombinedOutput(); err != nil {
 			lastErr = fmt.Errorf("%s: %v (%s)", rigName, err, string(output))

internal/templates/roles/crew.md.tmpl

@@ -42,6 +42,7 @@ Town ({{ .TownRoot }})
 - Mail ALWAYS uses town beads - `gt mail` routes there automatically
 - Project issues use your clone's beads - `bd` commands use local `.beads/`
 - Run `bd sync` to push/pull beads changes via the `beads-sync` branch
+- **GitHub URLs**: Use `git remote -v` to verify repo URLs - never assume orgs like `anthropics/`
 
 ## Prefix-Based Routing
 

internal/templates/roles/deacon.md.tmpl

@@ -66,7 +66,7 @@ gt mail inbox
 gt mol attach-from-mail <mail-id>
 
 # Step 3: Still nothing? Create patrol wisp (two-step: create then pin)
-bd wisp create mol-deacon-patrol
+bd mol wisp create mol-deacon-patrol
 bd update <wisp-id> --status=pinned --assignee=deacon
 ```
 
@@ -135,7 +135,7 @@ Then squash and decide:
 bd mol squash <wisp-id> --summary="Patrol complete: checked inbox, scanned health, no issues"
 
 # Option A: Loop (low context)
-bd wisp create mol-deacon-patrol
+bd mol wisp create mol-deacon-patrol
 bd update <wisp-id> --status=pinned --assignee=deacon
 # Continue to first step...
 

internal/templates/roles/mayor.md.tmpl

@@ -68,6 +68,7 @@ Town ({{ .TownRoot }})
 - **Rig beads**: Project work lives in git worktrees (crew/*, polecats/*)
 - The rig-level `<rig>/.beads/` is **gitignored** (local runtime state)
 - Rig beads use `beads-sync` branch for multi-clone coordination
+- **GitHub URLs**: Use `git remote -v` to verify repo URLs - never assume orgs like `anthropics/`
 
 ## Prefix-Based Routing
 

internal/templates/roles/polecat.md.tmpl

@@ -39,6 +39,7 @@ Town ({{ .TownRoot }})
 - You're in a project git worktree - your `.beads/` is tracked in the project repo
 - The rig-level `{{ .RigName }}/.beads/` is **gitignored** (local runtime state)
 - Run `bd sync` to push/pull beads changes via the `beads-sync` branch
+- **GitHub URLs**: Use `git remote -v` to verify repo URLs - never assume orgs like `anthropics/`
 
 ## Prefix-Based Routing
 

internal/templates/roles/witness.md.tmpl

@@ -99,7 +99,7 @@ gt mail inbox
 gt mol attach-from-mail <mail-id>
 
 # Step 4: Still nothing? Create patrol wisp
-bd wisp mol-witness-patrol --assignee={{ .RigName }}/witness
+bd mol wisp mol-witness-patrol --assignee={{ .RigName }}/witness
 ```
 
 **Hook → Execute. No exceptions.**