bd sync: 2025-12-27 15:56:42

skills/beads/references/MOLECULES.md

@@ -55,11 +55,11 @@ bd mol distill bd-abc123 --as "Release Workflow" --var version=1.0.0
 
 **Proto naming convention:** Use `mol-` prefix for clarity (e.g., `mol-release`, `mol-patrol`).
 
-### Listing Formulas
+### Listing Protos
 
 ```bash
-bd formula list                 # List all formulas (protos)
-bd formula list --json          # Machine-readable
+bd mol catalog                  # List all protos
+bd mol catalog --json           # Machine-readable
 ```
 
 ### Viewing Proto Structure
@@ -83,8 +83,8 @@ bd mol spawn mol-release --var version=2.0 # With variable substitution
 
 **Chemistry shortcuts:**
 ```bash
-bd mol pour mol-feature                    # Shortcut for spawn --pour
-bd mol wisp mol-patrol                     # Explicit wisp creation
+bd pour mol-feature                        # Shortcut for spawn --pour
+bd wisp create mol-patrol                  # Explicit wisp creation
 ```
 
 ### Spawn with Immediate Execution
@@ -164,7 +164,7 @@ bd mol bond mol-feature mol-deploy --as "Feature with Deploy"
 ### Creating Wisps
 
 ```bash
-bd mol wisp mol-patrol                       # From proto
+bd wisp create mol-patrol                    # From proto
 bd mol spawn mol-patrol                      # Same (spawn defaults to wisp)
 bd mol spawn mol-check --var target=db       # With variables
 ```
@@ -172,8 +172,8 @@ bd mol spawn mol-check --var target=db       # With variables
 ### Listing Wisps
 
 ```bash
-bd mol wisp list                     # List all wisps
-bd mol wisp list --json              # Machine-readable
+bd wisp list                    # List all wisps
+bd wisp list --json             # Machine-readable
 ```
 
 ### Ending Wisps
@@ -198,7 +198,7 @@ Use burn for routine work with no archival value.
 ### Garbage Collection
 
 ```bash
-bd mol wisp gc                       # Clean up orphaned wisps
+bd wisp gc                      # Clean up orphaned wisps
 ```
 
 ---
@@ -289,7 +289,7 @@ bd mol spawn mol-weekly-review --pour
 
 ```bash
 # Patrol proto exists
-bd mol wisp mol-patrol
+bd wisp create mol-patrol
 
 # Execute patrol work...
 
@@ -318,7 +318,7 @@ bd mol distill bd-release-epic --as "Release Process" --var version=X.Y.Z
 
 | Command | Purpose |
 |---------|---------|
-| `bd formula list` | List available formulas/protos |
+| `bd mol catalog` | List available protos |
 | `bd mol show <id>` | Show proto/mol structure |
 | `bd mol spawn <proto>` | Create wisp from proto (default) |
 | `bd mol spawn <proto> --pour` | Create persistent mol from proto |
@@ -327,10 +327,10 @@ bd mol distill bd-release-epic --as "Release Process" --var version=X.Y.Z
 | `bd mol distill <epic>` | Extract proto from ad-hoc work |
 | `bd mol squash <mol>` | Compress wisp children to digest |
 | `bd mol burn <wisp>` | Delete wisp without trace |
-| `bd mol pour <proto>` | Shortcut for `spawn --pour` |
-| `bd mol wisp <proto>` | Create ephemeral wisp |
-| `bd mol wisp list` | List all wisps |
-| `bd mol wisp gc` | Garbage collect orphaned wisps |
+| `bd pour <proto>` | Shortcut for `spawn --pour` |
+| `bd wisp create <proto>` | Create ephemeral wisp |
+| `bd wisp list` | List all wisps |
+| `bd wisp gc` | Garbage collect orphaned wisps |
 | `bd ship <capability>` | Publish capability for cross-project deps |
 
 ---
@@ -338,7 +338,7 @@ bd mol distill bd-release-epic --as "Release Process" --var version=X.Y.Z
 ## Troubleshooting
 
 **"Proto not found"**
-- Check `bd formula list` for available formulas/protos
+- Check `bd mol catalog` for available protos
 - Protos need `template` label on the epic
 
 **"Variable not substituted"**
@@ -347,7 +347,7 @@ bd mol distill bd-release-epic --as "Release Process" --var version=X.Y.Z
 
 **"Wisp commands fail"**
 - Wisps stored in `.beads-wisp/` (separate from `.beads/`)
-- Check `bd mol wisp list` for active wisps
+- Check `bd wisp list` for active wisps
 
 **"External dependency not satisfied"**
 - Target project must have closed issue with `provides:<capability>` label