Update documentation for bd mol pour/wisp command structure

Updated all documentation and help text to reflect:
- bd pour → bd mol pour
- bd ephemeral → bd mol wisp
- bd ephemeral list → bd mol wisp list
- bd ephemeral gc → bd mol wisp gc

Files updated:
- docs/MOLECULES.md
- docs/CLI_REFERENCE.md
- docs/ARCHITECTURE.md
- docs/DELETIONS.md
- skills/beads/references/MOLECULES.md
- cmd/bd/mol_catalog.go
- cmd/bd/mol_current.go
- cmd/bd/mol_distill.go
- cmd/bd/cook.go

skills/beads/references/MOLECULES.md

@@ -83,8 +83,8 @@ bd mol spawn mol-release --var version=2.0 # With variable substitution
 
 **Chemistry shortcuts:**
 ```bash
-bd pour mol-feature                        # Shortcut for spawn --pour
-bd ephemeral create mol-patrol                  # Explicit wisp creation
+bd mol pour mol-feature                    # Shortcut for spawn --pour
+bd mol wisp 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 ephemeral create mol-patrol                    # From proto
+bd mol wisp 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 ephemeral list                    # List all wisps
-bd ephemeral list --json             # Machine-readable
+bd mol wisp list                     # List all wisps
+bd mol wisp list --json              # Machine-readable
 ```
 
 ### Ending Wisps
@@ -198,7 +198,7 @@ Use burn for routine work with no archival value.
 ### Garbage Collection
 
 ```bash
-bd ephemeral gc                      # Clean up orphaned wisps
+bd mol wisp gc                       # Clean up orphaned wisps
 ```
 
 ---
@@ -289,7 +289,7 @@ bd mol spawn mol-weekly-review --pour
 
 ```bash
 # Patrol proto exists
-bd ephemeral create mol-patrol
+bd mol wisp mol-patrol
 
 # Execute patrol work...
 
@@ -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 pour <proto>` | Shortcut for `spawn --pour` |
-| `bd ephemeral create <proto>` | Create ephemeral wisp |
-| `bd ephemeral list` | List all wisps |
-| `bd ephemeral gc` | Garbage collect orphaned wisps |
+| `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 ship <capability>` | Publish capability for cross-project deps |
 
 ---
@@ -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 ephemeral list` for active wisps
+- Check `bd mol wisp list` for active wisps
 
 **"External dependency not satisfied"**
 - Target project must have closed issue with `provides:<capability>` label