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

cmd/bd/cook.go

@@ -353,7 +353,7 @@ func runCook(cmd *cobra.Command, args []string) {
 	if len(bondPoints) > 0 {
 		fmt.Printf("  Bond points: %s\n", strings.Join(bondPoints, ", "))
 	}
-	fmt.Printf("\nTo use: bd pour %s --var <name>=<value>\n", result.ProtoID)
+	fmt.Printf("\nTo use: bd mol pour %s --var <name>=<value>\n", result.ProtoID)
 }
 
 // cookFormulaResult holds the result of cooking

cmd/bd/mol_catalog.go

@@ -23,7 +23,7 @@ var molCatalogCmd = &cobra.Command{
 	Use:     "catalog",
 	Aliases: []string{"list", "ls"},
 	Short:   "List available molecule formulas",
-	Long: `List formulas available for bd pour / bd ephemeral create.
+	Long: `List formulas available for bd mol pour / bd mol wisp.
 
 Formulas are ephemeral proto definitions stored as .formula.json files.
 They are cooked inline when pouring, never stored as database beads.
@@ -92,12 +92,12 @@ Search paths (in priority order):
 			fmt.Println("\nOr distill from existing work:")
 			fmt.Println("  bd mol distill <epic-id> my-workflow")
 			fmt.Println("\nTo instantiate from formula:")
-			fmt.Println("  bd pour <formula-name> --var key=value          # persistent mol")
-			fmt.Println("  bd ephemeral create <formula-name> --var key=value   # ephemeral wisp")
+			fmt.Println("  bd mol pour <formula-name> --var key=value      # persistent mol")
+			fmt.Println("  bd mol wisp <formula-name> --var key=value      # ephemeral wisp")
 			return
 		}
 
-		fmt.Printf("%s\n\n", ui.RenderPass("Formulas (for bd pour / bd ephemeral create):"))
+		fmt.Printf("%s\n\n", ui.RenderPass("Formulas (for bd mol pour / bd mol wisp):"))
 
 		// Group by type for display
 		byType := make(map[string][]CatalogEntry)

cmd/bd/mol_current.go

@@ -100,7 +100,7 @@ The output shows all steps with status indicators:
 				}
 				fmt.Println(".")
 				fmt.Println("\nTo start work on a molecule:")
-				fmt.Println("  bd pour <proto-id>          # Instantiate a molecule from template")
+				fmt.Println("  bd mol pour <proto-id>      # Instantiate a molecule from template")
 				fmt.Println("  bd update <step-id> --status in_progress  # Claim a step")
 				return
 			}

cmd/bd/mol_distill.go

@@ -225,7 +225,7 @@ func runMolDistill(cmd *cobra.Command, args []string) {
 		fmt.Printf("  Variables: %s\n", strings.Join(result.Variables, ", "))
 	}
 	fmt.Printf("\nTo instantiate:\n")
-	fmt.Printf("  bd pour %s", result.FormulaName)
+	fmt.Printf("  bd mol pour %s", result.FormulaName)
 	for _, v := range result.Variables {
 		fmt.Printf(" --var %s=<value>", v)
 	}