Fix comments display: move outside dependents block, merge main

cmd/bd/autoflush.go

@@ -671,7 +671,7 @@ func flushToJSONLWithState(state flushState) {
 	issues := make([]*types.Issue, 0, len(issueMap))
 	wispsSkipped := 0
 	for _, issue := range issueMap {
-		if issue.Wisp {
+		if issue.Ephemeral {
 			wispsSkipped++
 			continue
 		}

cmd/bd/cleanup.go

@@ -15,7 +15,7 @@ type CleanupEmptyResponse struct {
 	DeletedCount int    `json:"deleted_count"`
 	Message      string `json:"message"`
 	Filter       string `json:"filter,omitempty"`
-	Wisp         bool   `json:"wisp,omitempty"`
+	Ephemeral    bool   `json:"ephemeral,omitempty"`
 }
 
 // Hard delete mode: bypass tombstone TTL safety, use --older-than days directly
@@ -56,7 +56,7 @@ Delete issues closed more than 30 days ago:
   bd cleanup --older-than 30 --force
 
 Delete only closed wisps (transient molecules):
-  bd cleanup --wisp --force
+  bd cleanup --ephemeral --force
 
 Preview what would be deleted/pruned:
   bd cleanup --dry-run
@@ -80,7 +80,7 @@ SEE ALSO:
 		cascade, _ := cmd.Flags().GetBool("cascade")
 		olderThanDays, _ := cmd.Flags().GetInt("older-than")
 		hardDelete, _ := cmd.Flags().GetBool("hard")
-		wispOnly, _ := cmd.Flags().GetBool("wisp")
+		wispOnly, _ := cmd.Flags().GetBool("ephemeral")
 
 		// Calculate custom TTL for --hard mode
 		// When --hard is set, use --older-than days as the tombstone TTL cutoff
@@ -129,7 +129,7 @@ SEE ALSO:
 		// Add wisp filter if specified (bd-kwro.9)
 		if wispOnly {
 			wispTrue := true
-			filter.Wisp = &wispTrue
+			filter.Ephemeral = &wispTrue
 		}
 
 		// Get all closed issues matching filter
@@ -165,7 +165,7 @@ SEE ALSO:
 					result.Filter = fmt.Sprintf("older than %d days", olderThanDays)
 				}
 				if wispOnly {
-					result.Wisp = true
+					result.Ephemeral = true
 				}
 				outputJSON(result)
 			} else {
@@ -270,6 +270,6 @@ func init() {
 	cleanupCmd.Flags().Bool("cascade", false, "Recursively delete all dependent issues")
 	cleanupCmd.Flags().Int("older-than", 0, "Only delete issues closed more than N days ago (0 = all closed issues)")
 	cleanupCmd.Flags().Bool("hard", false, "Bypass tombstone TTL safety; use --older-than days as cutoff")
-	cleanupCmd.Flags().Bool("wisp", false, "Only delete closed wisps (transient molecules)")
+	cleanupCmd.Flags().Bool("ephemeral", false, "Only delete closed wisps (transient molecules)")
 	rootCmd.AddCommand(cleanupCmd)
 }

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/create.go

@@ -107,7 +107,7 @@ var createCmd = &cobra.Command{
 		waitsForGate, _ := cmd.Flags().GetString("waits-for-gate")
 		forceCreate, _ := cmd.Flags().GetBool("force")
 		repoOverride, _ := cmd.Flags().GetString("repo")
-		wisp, _ := cmd.Flags().GetBool("wisp")
+		wisp, _ := cmd.Flags().GetBool("ephemeral")
 
 		// Get estimate if provided
 		var estimatedMinutes *int
@@ -222,7 +222,7 @@ var createCmd = &cobra.Command{
 				Dependencies:       deps,
 				WaitsFor:           waitsFor,
 				WaitsForGate:       waitsForGate,
-				Wisp:               wisp,
+				Ephemeral:          wisp,
 				CreatedBy:          getActorWithGit(),
 			}
 
@@ -268,7 +268,7 @@ var createCmd = &cobra.Command{
 			Assignee:           assignee,
 			ExternalRef:        externalRefPtr,
 			EstimatedMinutes:   estimatedMinutes,
-			Wisp:               wisp,
+			Ephemeral:          wisp,
 			CreatedBy:          getActorWithGit(), // GH#748: track who created the issue
 		}
 
@@ -448,7 +448,7 @@ func init() {
 	createCmd.Flags().Bool("force", false, "Force creation even if prefix doesn't match database prefix")
 	createCmd.Flags().String("repo", "", "Target repository for issue (overrides auto-routing)")
 	createCmd.Flags().IntP("estimate", "e", 0, "Time estimate in minutes (e.g., 60 for 1 hour)")
-	createCmd.Flags().Bool("wisp", false, "Create as wisp (ephemeral, not exported to JSONL)")
+	createCmd.Flags().Bool("ephemeral", false, "Create as ephemeral (ephemeral, not exported to JSONL)")
 	// Note: --json flag is defined as a persistent flag in main.go, not here
 	rootCmd.AddCommand(createCmd)
 }

cmd/bd/dep.go

@@ -5,9 +5,11 @@ import (
 	"encoding/json"
 	"fmt"
 	"os"
+	"path/filepath"
 	"strings"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/routing"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
@@ -15,6 +17,14 @@ import (
 	"github.com/steveyegge/beads/internal/utils"
 )
 
+// getBeadsDir returns the .beads directory path, derived from the global dbPath.
+func getBeadsDir() string {
+	if dbPath != "" {
+		return filepath.Dir(dbPath)
+	}
+	return ""
+}
+
 // isChildOf returns true if childID is a hierarchical child of parentID.
 // For example, "bd-abc.1" is a child of "bd-abc", and "bd-abc.1.2" is a child of "bd-abc.1".
 func isChildOf(childID, parentID string) bool {
@@ -88,9 +98,15 @@ Examples:
 				resolveArgs = &rpc.ResolveIDArgs{ID: args[1]}
 				resp, err = daemonClient.ResolveID(resolveArgs)
 				if err != nil {
-					FatalErrorRespectJSON("resolving dependency ID %s: %v", args[1], err)
+					// Resolution failed - try auto-converting to external ref (bd-lfiu)
-				}
+					beadsDir := getBeadsDir()
-				if err := json.Unmarshal(resp.Data, &toID); err != nil {
+					if extRef := routing.ResolveToExternalRef(args[1], beadsDir); extRef != "" {
+						toID = extRef
+						isExternalRef = true
+					} else {
+						FatalErrorRespectJSON("resolving dependency ID %s: %v", args[1], err)
+					}
+				} else if err := json.Unmarshal(resp.Data, &toID); err != nil {
 					FatalErrorRespectJSON("unmarshaling resolved ID: %v", err)
 				}
 			}
@@ -111,7 +127,14 @@ Examples:
 			} else {
 				toID, err = utils.ResolvePartialID(ctx, store, args[1])
 				if err != nil {
-					FatalErrorRespectJSON("resolving dependency ID %s: %v", args[1], err)
+					// Resolution failed - try auto-converting to external ref (bd-lfiu)
+					beadsDir := getBeadsDir()
+					if extRef := routing.ResolveToExternalRef(args[1], beadsDir); extRef != "" {
+						toID = extRef
+						isExternalRef = true
+					} else {
+						FatalErrorRespectJSON("resolving dependency ID %s: %v", args[1], err)
+					}
 				}
 			}
 		}

cmd/bd/export.go

@@ -362,7 +362,7 @@ Examples:
 		// Wisps exist only in SQLite and are shared via .beads/redirect, not JSONL.
 		filtered := make([]*types.Issue, 0, len(issues))
 		for _, issue := range issues {
-			if !issue.Wisp {
+			if !issue.Ephemeral {
 				filtered = append(filtered, issue)
 			}
 		}

cmd/bd/gate.go

@@ -157,7 +157,7 @@ Examples:
 				Status:    types.StatusOpen,
 				Priority:  1, // Gates are typically high priority
 				// Assignee left empty - orchestrator decides who processes gates
-				Wisp:      true, // Gates are wisps (ephemeral)
+				Ephemeral:      true, // Gates are wisps (ephemeral)
 				AwaitType: awaitType,
 				AwaitID:   awaitID,
 				Timeout:   timeout,

cmd/bd/hook.go

@@ -87,8 +87,8 @@ func runHook(cmd *cobra.Command, args []string) {
 
 	for _, issue := range issues {
 		phase := "mol"
-		if issue.Wisp {
+		if issue.Ephemeral {
-			phase = "wisp"
+			phase = "ephemeral"
 		}
 		fmt.Printf("  📌 %s (%s) - %s\n", issue.ID, phase, issue.Status)
 		fmt.Printf("     %s\n", issue.Title)

cmd/bd/info.go

@@ -292,6 +292,7 @@ var versionChanges = []VersionChange{
 		Version: "0.37.0",
 		Date:    "2025-12-26",
 		Changes: []string{
+			"BREAKING: Ephemeral API rename (bd-o18s) - Wisp→Ephemeral: JSON 'wisp'→'ephemeral', bd wisp→bd ephemeral",
 			"NEW: bd gate create/show/list/close/wait (bd-udsi) - Async coordination primitives for agent workflows",
 			"NEW: bd gate eval (gt-twjr5.2) - Evaluate timer gates and GitHub gates (gh:run, gh:pr, mail)",
 			"NEW: bd gate approve (gt-twjr5.4) - Human gate approval command",

cmd/bd/mol.go

@@ -20,8 +20,8 @@ import (
 // Usage:
 //   bd mol catalog                        # List available protos
 //   bd mol show <id>                      # Show proto/molecule structure
-//   bd pour <id> --var key=value          # Instantiate proto → persistent mol
+//   bd mol pour <id> --var key=value      # Instantiate proto → persistent mol
-//   bd wisp create <id> --var key=value   # Instantiate proto → ephemeral wisp
+//   bd mol wisp <id> --var key=value      # Instantiate proto → ephemeral wisp
 
 // MoleculeLabel is the label used to identify molecules (templates)
 // Molecules use the same label as templates - they ARE templates with workflow semantics
@@ -48,14 +48,14 @@ The molecule metaphor:
   - Distilling extracts a proto from an ad-hoc epic
 
 Commands:
-  catalog  List available protos
+  catalog    List available protos
-  show     Show proto/molecule structure and variables
+  show       Show proto/molecule structure and variables
-  bond     Polymorphic combine: proto+proto, proto+mol, mol+mol
+  pour       Instantiate proto as persistent mol (liquid phase)
-  distill  Extract proto from ad-hoc epic
+  wisp       Instantiate proto as ephemeral wisp (vapor phase)
-
+  bond       Polymorphic combine: proto+proto, proto+mol, mol+mol
-See also:
+  squash     Condense molecule to digest
-  bd pour <proto>          # Instantiate as persistent mol (liquid phase)
+  burn       Discard wisp
-  bd wisp create <proto>   # Instantiate as ephemeral wisp (vapor phase)`,
+  distill    Extract proto from ad-hoc epic`,
 }
 
 // =============================================================================
@@ -72,7 +72,7 @@ func spawnMolecule(ctx context.Context, s storage.Storage, subgraph *MoleculeSub
 		Vars:     vars,
 		Assignee: assignee,
 		Actor:    actorName,
-		Wisp:     ephemeral,
+		Ephemeral:     ephemeral,
 		Prefix:   prefix,
 	}
 	return cloneSubgraph(ctx, s, subgraph, opts)

cmd/bd/mol_bond.go

@@ -40,12 +40,12 @@ Bond types:
 
 Phase control:
   By default, spawned protos follow the target's phase:
-  - Attaching to mol (Wisp=false) → spawns as persistent (Wisp=false)
+  - Attaching to mol (Ephemeral=false) → spawns as persistent (Ephemeral=false)
-  - Attaching to wisp (Wisp=true) → spawns as ephemeral (Wisp=true)
+  - Attaching to ephemeral issue (Ephemeral=true) → spawns as ephemeral (Ephemeral=true)
 
   Override with:
-  --pour  Force spawn as liquid (persistent, Wisp=false)
+  --pour  Force spawn as liquid (persistent, Ephemeral=false)
-  --wisp  Force spawn as vapor (ephemeral, Wisp=true, excluded from JSONL export)
+  --ephemeral  Force spawn as vapor (ephemeral, Ephemeral=true, excluded from JSONL export)
 
 Dynamic bonding (Christmas Ornament pattern):
   Use --ref to specify a custom child reference with variable substitution.
@@ -57,7 +57,7 @@ Dynamic bonding (Christmas Ornament pattern):
 
 Use cases:
   - Found important bug during patrol? Use --pour to persist it
-  - Need ephemeral diagnostic on persistent feature? Use --wisp
+  - Need ephemeral diagnostic on persistent feature? Use --ephemeral
   - Spawning per-worker arms on a patrol? Use --ref for readable IDs
 
 Examples:
@@ -66,7 +66,7 @@ Examples:
   bd mol bond mol-feature bd-abc123                     # Attach proto to molecule
   bd mol bond bd-abc123 bd-def456                       # Join two molecules
   bd mol bond mol-critical-bug wisp-patrol --pour       # Persist found bug
-  bd mol bond mol-temp-check bd-feature --wisp          # Ephemeral diagnostic
+  bd mol bond mol-temp-check bd-feature --ephemeral          # Ephemeral diagnostic
   bd mol bond mol-arm bd-patrol --ref arm-{{name}} --var name=ace  # Dynamic child ID`,
 	Args: cobra.ExactArgs(2),
 	Run:  runMolBond,
@@ -102,20 +102,20 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	customTitle, _ := cmd.Flags().GetString("as")
 	dryRun, _ := cmd.Flags().GetBool("dry-run")
 	varFlags, _ := cmd.Flags().GetStringSlice("var")
-	wisp, _ := cmd.Flags().GetBool("wisp")
+	ephemeral, _ := cmd.Flags().GetBool("ephemeral")
 	pour, _ := cmd.Flags().GetBool("pour")
 	childRef, _ := cmd.Flags().GetString("ref")
 
 	// Validate phase flags are not both set
-	if wisp && pour {
+	if ephemeral && pour {
-		fmt.Fprintf(os.Stderr, "Error: cannot use both --wisp and --pour\n")
+		fmt.Fprintf(os.Stderr, "Error: cannot use both --ephemeral and --pour\n")
 		os.Exit(1)
 	}
 
-	// All issues go in the main store; wisp vs pour determines the Wisp flag
+	// All issues go in the main store; ephemeral vs pour determines the Wisp flag
-	// --wisp: create with Wisp=true (ephemeral, excluded from JSONL export)
+	// --ephemeral: create with Ephemeral=true (ephemeral, excluded from JSONL export)
-	// --pour: create with Wisp=false (persistent, exported to JSONL)
+	// --pour: create with Ephemeral=false (persistent, exported to JSONL)
-	// Default: follow target's phase (wisp if target is wisp, otherwise persistent)
+	// Default: follow target's phase (ephemeral if target is ephemeral, otherwise persistent)
 
 	// Validate bond type
 	if bondType != types.BondTypeSequential && bondType != types.BondTypeParallel && bondType != types.BondTypeConditional {
@@ -181,8 +181,8 @@ func runMolBond(cmd *cobra.Command, args []string) {
 			fmt.Printf("  B: %s (%s)\n", issueB.Title, operandType(bIsProto))
 		}
 		fmt.Printf("  Bond type: %s\n", bondType)
-		if wisp {
+		if ephemeral {
-			fmt.Printf("  Phase override: vapor (--wisp)\n")
+			fmt.Printf("  Phase override: vapor (--ephemeral)\n")
 		} else if pour {
 			fmt.Printf("  Phase override: liquid (--pour)\n")
 		}
@@ -240,16 +240,16 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	case aIsProto && !bIsProto:
 		// Pass subgraph directly if cooked from formula
 		if cookedA {
-			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphA, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphA, issueA, issueB, bondType, vars, childRef, actor, ephemeral, pour)
 		} else {
-			result, err = bondProtoMol(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+			result, err = bondProtoMol(ctx, store, issueA, issueB, bondType, vars, childRef, actor, ephemeral, pour)
 		}
 	case !aIsProto && bIsProto:
 		// Pass subgraph directly if cooked from formula
 		if cookedB {
-			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphB, issueB, issueA, bondType, vars, childRef, actor, wisp, pour)
+			result, err = bondProtoMolWithSubgraph(ctx, store, subgraphB, issueB, issueA, bondType, vars, childRef, actor, ephemeral, pour)
 		} else {
-			result, err = bondMolProto(ctx, store, issueA, issueB, bondType, vars, childRef, actor, wisp, pour)
+			result, err = bondMolProto(ctx, store, issueA, issueB, bondType, vars, childRef, actor, ephemeral, pour)
 		}
 	default:
 		result, err = bondMolMol(ctx, store, issueA, issueB, bondType, actor)
@@ -273,10 +273,10 @@ func runMolBond(cmd *cobra.Command, args []string) {
 	if result.Spawned > 0 {
 		fmt.Printf("  Spawned: %d issues\n", result.Spawned)
 	}
-	if wisp {
+	if ephemeral {
-		fmt.Printf("  Phase: vapor (ephemeral, Wisp=true)\n")
+		fmt.Printf("  Phase: vapor (ephemeral, Ephemeral=true)\n")
 	} else if pour {
-		fmt.Printf("  Phase: liquid (persistent, Wisp=false)\n")
+		fmt.Printf("  Phase: liquid (persistent, Ephemeral=false)\n")
 	}
 }
 
@@ -386,12 +386,12 @@ func bondProtoProto(ctx context.Context, s storage.Storage, protoA, protoB *type
 // bondProtoMol bonds a proto to an existing molecule by spawning the proto.
 // If childRef is provided, generates custom IDs like "parent.childref" (dynamic bonding).
 // protoSubgraph can be nil if proto is from DB (will be loaded), or pre-loaded for formulas.
-func bondProtoMol(ctx context.Context, s storage.Storage, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, wispFlag, pourFlag bool) (*BondResult, error) {
+func bondProtoMol(ctx context.Context, s storage.Storage, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, ephemeralFlag, pourFlag bool) (*BondResult, error) {
-	return bondProtoMolWithSubgraph(ctx, s, nil, proto, mol, bondType, vars, childRef, actorName, wispFlag, pourFlag)
+	return bondProtoMolWithSubgraph(ctx, s, nil, proto, mol, bondType, vars, childRef, actorName, ephemeralFlag, pourFlag)
 }
 
 // bondProtoMolWithSubgraph is the internal implementation that accepts a pre-loaded subgraph.
-func bondProtoMolWithSubgraph(ctx context.Context, s storage.Storage, protoSubgraph *TemplateSubgraph, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, wispFlag, pourFlag bool) (*BondResult, error) {
+func bondProtoMolWithSubgraph(ctx context.Context, s storage.Storage, protoSubgraph *TemplateSubgraph, proto, mol *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, ephemeralFlag, pourFlag bool) (*BondResult, error) {
 	// Use provided subgraph or load from DB
 	subgraph := protoSubgraph
 	if subgraph == nil {
@@ -414,20 +414,20 @@ func bondProtoMolWithSubgraph(ctx context.Context, s storage.Storage, protoSubgr
 		return nil, fmt.Errorf("missing required variables: %s (use --var)", strings.Join(missingVars, ", "))
 	}
 
-	// Determine wisp flag based on explicit flags or target's phase
+	// Determine ephemeral flag based on explicit flags or target's phase
-	// --wisp: force wisp=true, --pour: force wisp=false, neither: follow target
+	// --ephemeral: force ephemeral=true, --pour: force ephemeral=false, neither: follow target
-	makeWisp := mol.Wisp // Default: follow target's phase
+	makeEphemeral := mol.Ephemeral // Default: follow target's phase
-	if wispFlag {
+	if ephemeralFlag {
-		makeWisp = true
+		makeEphemeral = true
 	} else if pourFlag {
-		makeWisp = false
+		makeEphemeral = false
 	}
 
 	// Build CloneOptions for spawning
 	opts := CloneOptions{
 		Vars:  vars,
 		Actor: actorName,
-		Wisp:  makeWisp,
+		Ephemeral:  makeEphemeral,
 	}
 
 	// Dynamic bonding: use custom IDs if childRef is provided
@@ -482,9 +482,9 @@ func bondProtoMolWithSubgraph(ctx context.Context, s storage.Storage, protoSubgr
 }
 
 // bondMolProto bonds a molecule to a proto (symmetric with bondProtoMol)
-func bondMolProto(ctx context.Context, s storage.Storage, mol, proto *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, wispFlag, pourFlag bool) (*BondResult, error) {
+func bondMolProto(ctx context.Context, s storage.Storage, mol, proto *types.Issue, bondType string, vars map[string]string, childRef string, actorName string, ephemeralFlag, pourFlag bool) (*BondResult, error) {
 	// Same as bondProtoMol but with arguments swapped
-	return bondProtoMol(ctx, s, proto, mol, bondType, vars, childRef, actorName, wispFlag, pourFlag)
+	return bondProtoMol(ctx, s, proto, mol, bondType, vars, childRef, actorName, ephemeralFlag, pourFlag)
 }
 
 // bondMolMol bonds two molecules together
@@ -630,8 +630,8 @@ func init() {
 	molBondCmd.Flags().String("as", "", "Custom title for compound proto (proto+proto only)")
 	molBondCmd.Flags().Bool("dry-run", false, "Preview what would be created")
 	molBondCmd.Flags().StringSlice("var", []string{}, "Variable substitution for spawned protos (key=value)")
-	molBondCmd.Flags().Bool("wisp", false, "Force spawn as vapor (ephemeral, Wisp=true)")
+	molBondCmd.Flags().Bool("ephemeral", false, "Force spawn as vapor (ephemeral, Ephemeral=true)")
-	molBondCmd.Flags().Bool("pour", false, "Force spawn as liquid (persistent, Wisp=false)")
+	molBondCmd.Flags().Bool("pour", false, "Force spawn as liquid (persistent, Ephemeral=false)")
 	molBondCmd.Flags().String("ref", "", "Custom child reference with {{var}} substitution (e.g., arm-{{polecat_name}})")
 
 	molCmd.AddCommand(molBondCmd)

cmd/bd/mol_burn.go

@@ -23,8 +23,8 @@ completely removes the wisp with no trace. Use this for:
   - Test/debug wisps you don't want to preserve
 
 The burn operation:
-  1. Verifies the molecule has Wisp=true (is ephemeral)
+  1. Verifies the molecule has Ephemeral=true (is ephemeral)
-  2. Deletes the molecule and all its wisp children
+  2. Deletes the molecule and all its ephemeral children
   3. No digest is created (use 'bd mol squash' if you want a digest)
 
 CAUTION: This is a destructive operation. The wisp's data will be
@@ -81,8 +81,8 @@ func runMolBurn(cmd *cobra.Command, args []string) {
 	}
 
 	// Verify it's a wisp
-	if !rootIssue.Wisp {
+	if !rootIssue.Ephemeral {
-		fmt.Fprintf(os.Stderr, "Error: molecule %s is not a wisp (Wisp=false)\n", resolvedID)
+		fmt.Fprintf(os.Stderr, "Error: molecule %s is not a wisp (Ephemeral=false)\n", resolvedID)
 		fmt.Fprintf(os.Stderr, "Hint: mol burn only works with wisp molecules\n")
 		fmt.Fprintf(os.Stderr, "      Use 'bd delete' to remove non-wisp issues\n")
 		os.Exit(1)
@@ -98,7 +98,7 @@ func runMolBurn(cmd *cobra.Command, args []string) {
 	// Collect wisp issue IDs to delete (only delete wisps, not regular children)
 	var wispIDs []string
 	for _, issue := range subgraph.Issues {
-		if issue.Wisp {
+		if issue.Ephemeral {
 			wispIDs = append(wispIDs, issue.ID)
 		}
 	}
@@ -120,7 +120,7 @@ func runMolBurn(cmd *cobra.Command, args []string) {
 		fmt.Printf("Root: %s\n", subgraph.Root.Title)
 		fmt.Printf("\nWisp issues to delete (%d total):\n", len(wispIDs))
 		for _, issue := range subgraph.Issues {
-			if !issue.Wisp {
+			if !issue.Ephemeral {
 				continue
 			}
 			status := string(issue.Status)
@@ -166,7 +166,7 @@ func runMolBurn(cmd *cobra.Command, args []string) {
 	}
 
 	fmt.Printf("%s Burned wisp: %d issues deleted\n", ui.RenderPass("✓"), result.DeletedCount)
-	fmt.Printf("  Wisp: %s\n", resolvedID)
+	fmt.Printf("  Ephemeral: %s\n", resolvedID)
 	fmt.Printf("  No digest created.\n")
 }
 

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 wisp 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 mol pour <formula-name> --var key=value      # persistent mol")
-			fmt.Println("  bd wisp create <formula-name> --var key=value   # ephemeral wisp")
+			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 wisp 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)
 	}

cmd/bd/mol_squash.go

@@ -18,17 +18,17 @@ import (
 var molSquashCmd = &cobra.Command{
 	Use:   "squash <molecule-id>",
 	Short: "Compress molecule execution into a digest",
-	Long: `Squash a molecule's wisp children into a single digest issue.
+	Long: `Squash a molecule's ephemeral children into a single digest issue.
 
-This command collects all wisp child issues of a molecule (Wisp=true),
+This command collects all ephemeral child issues of a molecule (Ephemeral=true),
 generates a summary digest, and promotes the wisps to persistent by
 clearing their Wisp flag (or optionally deletes them).
 
 The squash operation:
   1. Loads the molecule and all its children
-  2. Filters to only wisps (ephemeral issues with Wisp=true)
+  2. Filters to only wisps (ephemeral issues with Ephemeral=true)
   3. Generates a digest (summary of work done)
-  4. Creates a permanent digest issue (Wisp=false)
+  4. Creates a permanent digest issue (Ephemeral=false)
   5. Clears Wisp flag on children (promotes to persistent)
      OR deletes them with --delete-children
 
@@ -95,13 +95,13 @@ func runMolSquash(cmd *cobra.Command, args []string) {
 		os.Exit(1)
 	}
 
-	// Filter to only wisp children (exclude root)
+	// Filter to only ephemeral children (exclude root)
 	var wispChildren []*types.Issue
 	for _, issue := range subgraph.Issues {
 		if issue.ID == subgraph.Root.ID {
 			continue // Skip root
 		}
-		if issue.Wisp {
+		if issue.Ephemeral {
 			wispChildren = append(wispChildren, issue)
 		}
 	}
@@ -113,13 +113,13 @@ func runMolSquash(cmd *cobra.Command, args []string) {
 				SquashedCount: 0,
 			})
 		} else {
-			fmt.Printf("No wisp children found for molecule %s\n", moleculeID)
+			fmt.Printf("No ephemeral children found for molecule %s\n", moleculeID)
 		}
 		return
 	}
 
 	if dryRun {
-		fmt.Printf("\nDry run: would squash %d wisp children of %s\n\n", len(wispChildren), moleculeID)
+		fmt.Printf("\nDry run: would squash %d ephemeral children of %s\n\n", len(wispChildren), moleculeID)
 		fmt.Printf("Root: %s\n", subgraph.Root.Title)
 		fmt.Printf("\nWisp children to squash:\n")
 		for _, issue := range wispChildren {
@@ -247,7 +247,7 @@ func squashMolecule(ctx context.Context, s storage.Storage, root *types.Issue, c
 		CloseReason: fmt.Sprintf("Squashed from %d wisps", len(children)),
 		Priority:    root.Priority,
 		IssueType:   types.TypeTask,
-		Wisp:        false, // Digest is permanent, not a wisp
+		Ephemeral:        false, // Digest is permanent, not a wisp
 		ClosedAt:    &now,
 	}
 
@@ -283,7 +283,7 @@ func squashMolecule(ctx context.Context, s storage.Storage, root *types.Issue, c
 		return nil, err
 	}
 
-	// Delete wisp children (outside transaction for better error handling)
+	// Delete ephemeral children (outside transaction for better error handling)
 	if !keepChildren {
 		deleted, err := deleteWispChildren(ctx, s, childIDs)
 		if err != nil {
@@ -319,7 +319,7 @@ func deleteWispChildren(ctx context.Context, s storage.Storage, ids []string) (i
 
 func init() {
 	molSquashCmd.Flags().Bool("dry-run", false, "Preview what would be squashed")
-	molSquashCmd.Flags().Bool("keep-children", false, "Don't delete wisp children after squash")
+	molSquashCmd.Flags().Bool("keep-children", false, "Don't delete ephemeral children after squash")
 	molSquashCmd.Flags().String("summary", "", "Agent-provided summary (bypasses auto-generation)")
 
 	molCmd.AddCommand(molSquashCmd)

cmd/bd/mol_test.go

@@ -489,7 +489,7 @@ func TestSquashMolecule(t *testing.T) {
 		Status:      types.StatusClosed,
 		Priority:    2,
 		IssueType:   types.TypeTask,
-		Wisp:        true,
+		Ephemeral:        true,
 		CloseReason: "Completed design",
 	}
 	child2 := &types.Issue{
@@ -498,7 +498,7 @@ func TestSquashMolecule(t *testing.T) {
 		Status:      types.StatusClosed,
 		Priority:    2,
 		IssueType:   types.TypeTask,
-		Wisp:        true,
+		Ephemeral:        true,
 		CloseReason: "Code merged",
 	}
 
@@ -547,7 +547,7 @@ func TestSquashMolecule(t *testing.T) {
 	if err != nil {
 		t.Fatalf("Failed to get digest: %v", err)
 	}
-	if digest.Wisp {
+	if digest.Ephemeral {
 		t.Error("Digest should NOT be ephemeral")
 	}
 	if digest.Status != types.StatusClosed {
@@ -595,7 +595,7 @@ func TestSquashMoleculeWithDelete(t *testing.T) {
 		Status:    types.StatusClosed,
 		Priority:  2,
 		IssueType: types.TypeTask,
-		Wisp:      true,
+		Ephemeral:      true,
 	}
 	if err := s.CreateIssue(ctx, child, "test"); err != nil {
 		t.Fatalf("Failed to create child: %v", err)
@@ -705,7 +705,7 @@ func TestSquashMoleculeWithAgentSummary(t *testing.T) {
 		Status:      types.StatusClosed,
 		Priority:    2,
 		IssueType:   types.TypeTask,
-		Wisp:        true,
+		Ephemeral:        true,
 		CloseReason: "Done",
 	}
 	if err := s.CreateIssue(ctx, child, "test"); err != nil {
@@ -1304,14 +1304,14 @@ func TestWispFilteringFromExport(t *testing.T) {
 		Status:    types.StatusOpen,
 		Priority:  1,
 		IssueType: types.TypeTask,
-		Wisp:      false,
+		Ephemeral:      false,
 	}
 	wispIssue := &types.Issue{
 		Title:     "Wisp Issue",
 		Status:    types.StatusOpen,
 		Priority:  2,
 		IssueType: types.TypeTask,
-		Wisp:      true,
+		Ephemeral:      true,
 	}
 
 	if err := s.CreateIssue(ctx, normalIssue, "test"); err != nil {
@@ -1333,7 +1333,7 @@ func TestWispFilteringFromExport(t *testing.T) {
 	// Filter wisp issues (simulating export behavior)
 	exportableIssues := make([]*types.Issue, 0)
 	for _, issue := range allIssues {
-		if !issue.Wisp {
+		if !issue.Ephemeral {
 			exportableIssues = append(exportableIssues, issue)
 		}
 	}

cmd/bd/nodb.go

@@ -72,8 +72,11 @@ func initializeNoDbMode() error {
 
 	debug.Logf("using prefix '%s'", prefix)
 
-	// Set global store
+	// Set global store and mark as active (fixes bd comment --no-db)
+	storeMutex.Lock()
 	store = memStore
+	storeActive = true
+	storeMutex.Unlock()
 	return nil
 }
 
@@ -218,7 +221,7 @@ func writeIssuesToJSONL(memStore *memory.MemoryStorage, beadsDir string) error {
 	// Wisps exist only in SQLite and are shared via .beads/redirect, not JSONL.
 	filtered := make([]*types.Issue, 0, len(issues))
 	for _, issue := range issues {
-		if !issue.Wisp {
+		if !issue.Ephemeral {
 			filtered = append(filtered, issue)
 		}
 	}

cmd/bd/nodb_test.go

@@ -158,6 +158,90 @@ func TestDetectPrefix(t *testing.T) {
 	})
 }
 
+func TestInitializeNoDbMode_SetsStoreActive(t *testing.T) {
+	// This test verifies the fix for bd comment --no-db not working.
+	// The bug was that initializeNoDbMode() set `store` but not `storeActive`,
+	// so ensureStoreActive() would try to find a SQLite database.
+
+	tempDir := t.TempDir()
+	beadsDir := filepath.Join(tempDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0o755); err != nil {
+		t.Fatalf("Failed to create .beads dir: %v", err)
+	}
+
+	// Create a minimal JSONL file with one issue
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	content := `{"id":"bd-1","title":"Test Issue","status":"open"}
+`
+	if err := os.WriteFile(jsonlPath, []byte(content), 0o600); err != nil {
+		t.Fatalf("Failed to write JSONL: %v", err)
+	}
+
+	// Save and restore global state
+	oldStore := store
+	oldStoreActive := storeActive
+	oldCwd, _ := os.Getwd()
+	defer func() {
+		storeMutex.Lock()
+		store = oldStore
+		storeActive = oldStoreActive
+		storeMutex.Unlock()
+		_ = os.Chdir(oldCwd)
+	}()
+
+	// Change to temp dir so initializeNoDbMode finds .beads
+	if err := os.Chdir(tempDir); err != nil {
+		t.Fatalf("Failed to chdir: %v", err)
+	}
+
+	// Reset global state
+	storeMutex.Lock()
+	store = nil
+	storeActive = false
+	storeMutex.Unlock()
+
+	// Initialize no-db mode
+	if err := initializeNoDbMode(); err != nil {
+		t.Fatalf("initializeNoDbMode failed: %v", err)
+	}
+
+	// Verify storeActive is now true
+	storeMutex.Lock()
+	active := storeActive
+	s := store
+	storeMutex.Unlock()
+
+	if !active {
+		t.Error("storeActive should be true after initializeNoDbMode")
+	}
+	if s == nil {
+		t.Fatal("store should not be nil after initializeNoDbMode")
+	}
+
+	// ensureStoreActive should now return immediately without error
+	if err := ensureStoreActive(); err != nil {
+		t.Errorf("ensureStoreActive should succeed after initializeNoDbMode: %v", err)
+	}
+
+	// Verify comments work (this was the failing case)
+	ctx := rootCtx
+	comment, err := s.AddIssueComment(ctx, "bd-1", "testuser", "Test comment")
+	if err != nil {
+		t.Fatalf("AddIssueComment failed: %v", err)
+	}
+	if comment.Text != "Test comment" {
+		t.Errorf("Expected 'Test comment', got %s", comment.Text)
+	}
+
+	comments, err := s.GetIssueComments(ctx, "bd-1")
+	if err != nil {
+		t.Fatalf("GetIssueComments failed: %v", err)
+	}
+	if len(comments) != 1 {
+		t.Errorf("Expected 1 comment, got %d", len(comments))
+	}
+}
+
 func TestWriteIssuesToJSONL(t *testing.T) {
 	tempDir := t.TempDir()
 	beadsDir := filepath.Join(tempDir, ".beads")

cmd/bd/pour.go

@@ -32,9 +32,9 @@ Use pour for:
   - Anything you might need to reference later
 
 Examples:
-  bd pour mol-feature --var name=auth    # Create persistent mol from proto
+  bd mol pour mol-feature --var name=auth    # Create persistent mol from proto
-  bd pour mol-release --var version=1.0  # Release workflow
+  bd mol pour mol-release --var version=1.0  # Release workflow
-  bd pour mol-review --var pr=123        # Code review workflow`,
+  bd mol pour mol-review --var pr=123        # Code review workflow`,
 	Args: cobra.ExactArgs(1),
 	Run:  runPour,
 }
@@ -260,5 +260,5 @@ func init() {
 	pourCmd.Flags().StringSlice("attach", []string{}, "Proto to attach after spawning (repeatable)")
 	pourCmd.Flags().String("attach-type", types.BondTypeSequential, "Bond type for attachments: sequential, parallel, or conditional")
 
-	rootCmd.AddCommand(pourCmd)
+	molCmd.AddCommand(pourCmd)
 }

cmd/bd/show.go

@@ -305,20 +305,20 @@ var showCmd = &cobra.Command{
 								fmt.Printf("  ◊ %s: %s [P%d - %s]\n", dep.ID, dep.Title, dep.Priority, dep.Status)
 							}
 						}
+					}
 
-						if len(details.Comments) > 0 {
+					if len(details.Comments) > 0 {
-							fmt.Printf("\nComments (%d):\n", len(details.Comments))
+						fmt.Printf("\nComments (%d):\n", len(details.Comments))
-							for _, comment := range details.Comments {
+						for _, comment := range details.Comments {
-								fmt.Printf("  [%s] %s\n", comment.Author, comment.CreatedAt.Format("2006-01-02 15:04"))
+							fmt.Printf("  [%s] %s\n", comment.Author, comment.CreatedAt.Format("2006-01-02 15:04"))
-								commentLines := strings.Split(comment.Text, "\n")
+							commentLines := strings.Split(comment.Text, "\n")
-								for _, line := range commentLines {
+							for _, line := range commentLines {
-									fmt.Printf("    %s\n", line)
+								fmt.Printf("    %s\n", line)
-								}
 							}
 						}
-						}
+					}
 
-						fmt.Println()
+					fmt.Println()
 				}
 			}
 

cmd/bd/sync_export.go

@@ -65,7 +65,7 @@ func exportToJSONL(ctx context.Context, jsonlPath string) error {
 	// This prevents "zombie" issues that resurrect after mol squash deletes them.
 	filteredIssues := make([]*types.Issue, 0, len(issues))
 	for _, issue := range issues {
-		if issue.Wisp {
+		if issue.Ephemeral {
 			continue
 		}
 		filteredIssues = append(filteredIssues, issue)

cmd/bd/template.go

@@ -42,10 +42,10 @@ type InstantiateResult struct {
 
 // CloneOptions controls how the subgraph is cloned during spawn/bond
 type CloneOptions struct {
-	Vars     map[string]string // Variable substitutions for {{key}} placeholders
+	Vars      map[string]string // Variable substitutions for {{key}} placeholders
-	Assignee string            // Assign the root epic to this agent/user
+	Assignee  string            // Assign the root epic to this agent/user
-	Actor    string            // Actor performing the operation
+	Actor     string            // Actor performing the operation
-	Wisp     bool              // If true, spawned issues are marked for bulk deletion
+	Ephemeral bool              // If true, spawned issues are marked for bulk deletion
 	Prefix   string            // Override prefix for ID generation (bd-hobo: distinct prefixes)
 
 	// Dynamic bonding fields (for Christmas Ornament pattern)
@@ -327,7 +327,7 @@ Example:
 			Vars:     vars,
 			Assignee: assignee,
 			Actor:    actor,
-			Wisp:     false,
+			Ephemeral:     false,
 		}
 		var result *InstantiateResult
 		if daemonClient != nil {
@@ -713,7 +713,7 @@ func cloneSubgraphViaDaemon(client *rpc.Client, subgraph *TemplateSubgraph, opts
 			AcceptanceCriteria: substituteVariables(oldIssue.AcceptanceCriteria, opts.Vars),
 			Assignee:           issueAssignee,
 			EstimatedMinutes:   oldIssue.EstimatedMinutes,
-			Wisp:               opts.Wisp,
+			Ephemeral:               opts.Ephemeral,
 			IDPrefix:           opts.Prefix, // bd-hobo: distinct prefixes for mols/wisps
 		}
 
@@ -960,7 +960,7 @@ func cloneSubgraph(ctx context.Context, s storage.Storage, subgraph *TemplateSub
 				IssueType:          oldIssue.IssueType,
 				Assignee:           issueAssignee,
 				EstimatedMinutes:   oldIssue.EstimatedMinutes,
-				Wisp:               opts.Wisp,   // bd-2vh3: mark for cleanup when closed
+				Ephemeral:               opts.Ephemeral,   // bd-2vh3: mark for cleanup when closed
 				IDPrefix:           opts.Prefix, // bd-hobo: distinct prefixes for mols/wisps
 				CreatedAt:          time.Now(),
 				UpdatedAt:          time.Now(),

cmd/bd/thread_test.go

@@ -27,7 +27,7 @@ func TestThreadTraversal(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "worker",
 		Sender:      "manager",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now,
 		UpdatedAt:   now,
 	}
@@ -43,7 +43,7 @@ func TestThreadTraversal(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "manager",
 		Sender:      "worker",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now.Add(time.Minute),
 		UpdatedAt:   now.Add(time.Minute),
 	}
@@ -59,7 +59,7 @@ func TestThreadTraversal(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "worker",
 		Sender:      "manager",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now.Add(2 * time.Minute),
 		UpdatedAt:   now.Add(2 * time.Minute),
 	}
@@ -190,7 +190,7 @@ func TestThreadTraversalEmptyThread(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "user",
 		Sender:      "sender",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now,
 		UpdatedAt:   now,
 	}
@@ -228,7 +228,7 @@ func TestThreadTraversalBranching(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "user",
 		Sender:      "sender",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now,
 		UpdatedAt:   now,
 	}
@@ -245,7 +245,7 @@ func TestThreadTraversalBranching(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "sender",
 		Sender:      "user",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now.Add(time.Minute),
 		UpdatedAt:   now.Add(time.Minute),
 	}
@@ -261,7 +261,7 @@ func TestThreadTraversalBranching(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "sender",
 		Sender:      "another-user",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now.Add(2 * time.Minute),
 		UpdatedAt:   now.Add(2 * time.Minute),
 	}
@@ -364,7 +364,7 @@ func TestThreadTraversalOnlyRepliesTo(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "user",
 		Sender:      "sender",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now,
 		UpdatedAt:   now,
 	}
@@ -380,7 +380,7 @@ func TestThreadTraversalOnlyRepliesTo(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Assignee:    "user",
 		Sender:      "sender",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   now.Add(time.Minute),
 		UpdatedAt:   now.Add(time.Minute),
 	}

cmd/bd/wisp.go

@@ -18,33 +18,43 @@ import (
 
 // Wisp commands - manage ephemeral molecules
 //
-// Wisps are ephemeral issues with Wisp=true in the main database.
+// Wisps are ephemeral issues with Ephemeral=true in the main database.
 // They're used for patrol cycles and operational loops that shouldn't
 // be exported to JSONL (and thus not synced via git).
 //
 // Commands:
-//   bd wisp list    - List all wisps in current context
+//   bd mol wisp list    - List all wisps in current context
-//   bd wisp gc      - Garbage collect orphaned wisps
+//   bd mol wisp gc      - Garbage collect orphaned wisps
 
 var wispCmd = &cobra.Command{
-	Use:   "wisp",
+	Use:   "wisp [proto-id]",
-	Short: "Manage ephemeral molecules (wisps)",
+	Short: "Create or manage wisps (ephemeral molecules)",
-	Long: `Manage wisps - ephemeral molecules for operational workflows.
+	Long: `Create or manage wisps - ephemeral molecules for operational workflows.
 
-Wisps are issues with Wisp=true in the main database. They're stored
+When called with a proto-id argument, creates a wisp from that proto.
+When called with a subcommand (list, gc), manages existing wisps.
+
+Wisps are issues with Ephemeral=true in the main database. They're stored
 locally but NOT exported to JSONL (and thus not synced via git).
 They're used for patrol cycles, operational loops, and other workflows
 that shouldn't accumulate in the shared issue database.
 
 The wisp lifecycle:
-  1. Create: bd wisp create <proto> or bd create --wisp
+  1. Create: bd mol wisp <proto> or bd create --ephemeral
-  2. Execute: Normal bd operations work on wisps
+  2. Execute: Normal bd operations work on wisp issues
-  3. Squash: bd mol squash <id> (clears Wisp flag, promotes to persistent)
+  3. Squash: bd mol squash <id> (clears Ephemeral flag, promotes to persistent)
-  4. Or burn: bd mol burn <id> (deletes wisp without creating digest)
+  4. Or burn: bd mol burn <id> (deletes without creating digest)
 
-Commands:
+Examples:
+  bd mol wisp mol-patrol             # Create wisp from proto
+  bd mol wisp list                   # List all wisps
+  bd mol wisp gc                     # Garbage collect old wisps
+
+Subcommands:
   list  List all wisps in current context
   gc    Garbage collect orphaned wisps`,
+	Args: cobra.MaximumNArgs(1),
+	Run:  runWisp,
 }
 
 // WispListItem represents a wisp in list output
@@ -68,32 +78,44 @@ type WispListResult struct {
 // OldThreshold is how old a wisp must be to be flagged as old (time-based, for ephemeral cleanup)
 const OldThreshold = 24 * time.Hour
 
-// wispCreateCmd instantiates a proto as an ephemeral wisp
+// runWisp handles the wisp command when called directly with a proto-id
+// It delegates to runWispCreate for the actual work
+func runWisp(cmd *cobra.Command, args []string) {
+	if len(args) == 0 {
+		// No proto-id provided, show help
+		cmd.Help()
+		return
+	}
+	// Delegate to the create logic
+	runWispCreate(cmd, args)
+}
+
+// wispCreateCmd instantiates a proto as an ephemeral wisp (kept for backwards compat)
 var wispCreateCmd = &cobra.Command{
 	Use:   "create <proto-id>",
-	Short: "Instantiate a proto as an ephemeral wisp (solid -> vapor)",
+	Short: "Instantiate a proto as a wisp (solid -> vapor)",
 	Long: `Create a wisp from a proto - sublimation from solid to vapor.
 
 This is the chemistry-inspired command for creating ephemeral work from templates.
-The resulting wisp is stored in the main database with Wisp=true and NOT exported to JSONL.
+The resulting wisp is stored in the main database with Ephemeral=true and NOT exported to JSONL.
 
 Phase transition: Proto (solid) -> Wisp (vapor)
 
-Use wisp create for:
+Use wisp for:
   - Patrol cycles (deacon, witness)
   - Health checks and monitoring
   - One-shot orchestration runs
   - Routine operations with no audit value
 
 The wisp will:
-  - Be stored in main database with Wisp=true flag
+  - Be stored in main database with Ephemeral=true flag
   - NOT be exported to JSONL (and thus not synced via git)
   - Either evaporate (burn) or condense to digest (squash)
 
 Examples:
-  bd wisp create mol-patrol                    # Ephemeral patrol cycle
+  bd mol wisp create mol-patrol                    # Ephemeral patrol cycle
-  bd wisp create mol-health-check              # One-time health check
+  bd mol wisp create mol-health-check              # One-time health check
-  bd wisp create mol-diagnostics --var target=db  # Diagnostic run`,
+  bd mol wisp create mol-diagnostics --var target=db  # Diagnostic run`,
 	Args: cobra.ExactArgs(1),
 	Run:  runWispCreate,
 }
@@ -107,7 +129,7 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 	if store == nil {
 		if daemonClient != nil {
 			fmt.Fprintf(os.Stderr, "Error: wisp create requires direct database access\n")
-			fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon wisp create %s ...\n", args[0])
+			fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon mol wisp %s ...\n", args[0])
 		} else {
 			fmt.Fprintf(os.Stderr, "Error: no database connection\n")
 		}
@@ -215,7 +237,7 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 
 	if dryRun {
 		fmt.Printf("\nDry run: would create wisp with %d issues from proto %s\n\n", len(subgraph.Issues), protoID)
-		fmt.Printf("Storage: main database (wisp=true, not exported to JSONL)\n\n")
+		fmt.Printf("Storage: main database (ephemeral=true, not exported to JSONL)\n\n")
 		for _, issue := range subgraph.Issues {
 			newTitle := substituteVariables(issue.Title, vars)
 			fmt.Printf("  - %s (from %s)\n", newTitle, issue.ID)
@@ -223,15 +245,15 @@ func runWispCreate(cmd *cobra.Command, args []string) {
 		return
 	}
 
-	// Spawn as wisp in main database (ephemeral=true sets Wisp flag, skips JSONL export)
+	// Spawn as ephemeral in main database (Ephemeral=true, skips JSONL export)
-	// bd-hobo: Use "wisp" prefix for distinct visual recognition
+	// bd-hobo: Use "eph" prefix for distinct visual recognition
-	result, err := spawnMolecule(ctx, store, subgraph, vars, "", actor, true, "wisp")
+	result, err := spawnMolecule(ctx, store, subgraph, vars, "", actor, true, "eph")
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "Error creating wisp: %v\n", err)
 		os.Exit(1)
 	}
 
-	// Wisps are in main db but don't trigger JSONL export (Wisp flag excludes them)
+	// Wisp issues are in main db but don't trigger JSONL export (Ephemeral flag excludes them)
 
 	if jsonOutput {
 		type wispCreateResult struct {
@@ -286,9 +308,9 @@ func resolvePartialIDDirect(ctx context.Context, partial string) (string, error)
 var wispListCmd = &cobra.Command{
 	Use:   "list",
 	Short: "List all wisps in current context",
-	Long: `List all ephemeral molecules (wisps) in the current context.
+	Long: `List all wisps (ephemeral molecules) in the current context.
 
-Wisps are issues with Wisp=true in the main database. They are stored
+Wisps are issues with Ephemeral=true in the main database. They are stored
 locally but not exported to JSONL (and thus not synced via git).
 
 The list shows:
@@ -300,12 +322,12 @@ The list shows:
 
 Old wisp detection:
   - Old wisps haven't been updated in 24+ hours
-  - Use 'bd wisp gc' to clean up old/abandoned wisps
+  - Use 'bd mol wisp gc' to clean up old/abandoned wisps
 
 Examples:
-  bd wisp list              # List all wisps
+  bd mol wisp list              # List all wisps
-  bd wisp list --json       # JSON output for programmatic use
+  bd mol wisp list --json       # JSON output for programmatic use
-  bd wisp list --all        # Include closed wisps`,
+  bd mol wisp list --all        # Include closed wisps`,
 	Run: runWispList,
 }
 
@@ -327,15 +349,15 @@ func runWispList(cmd *cobra.Command, args []string) {
 		return
 	}
 
-	// Query wisps from main database using Wisp filter
+	// Query wisps from main database using Ephemeral filter
-	wispFlag := true
+	ephemeralFlag := true
 	var issues []*types.Issue
 	var err error
 
 	if daemonClient != nil {
 		// Use daemon RPC
 		resp, rpcErr := daemonClient.List(&rpc.ListArgs{
-			Wisp: &wispFlag,
+			Ephemeral: &ephemeralFlag,
 		})
 		if rpcErr != nil {
 			err = rpcErr
@@ -347,7 +369,7 @@ func runWispList(cmd *cobra.Command, args []string) {
 	} else {
 		// Direct database access
 		filter := types.IssueFilter{
-			Wisp: &wispFlag,
+			Ephemeral: &ephemeralFlag,
 		}
 		issues, err = store.SearchIssues(ctx, "", filter)
 	}
@@ -444,7 +466,7 @@ func runWispList(cmd *cobra.Command, args []string) {
 	if oldCount > 0 {
 		fmt.Printf("\n%s %d old wisp(s) (not updated in 24+ hours)\n",
 			ui.RenderWarn("⚠"), oldCount)
-		fmt.Println("  Hint: Use 'bd wisp gc' to clean up old wisps")
+		fmt.Println("  Hint: Use 'bd mol wisp gc' to clean up old wisps")
 	}
 }
 
@@ -493,10 +515,10 @@ Note: This uses time-based cleanup, appropriate for ephemeral wisps.
 For graph-pressure staleness detection (blocking other work), see 'bd mol stale'.
 
 Examples:
-  bd wisp gc                # Clean abandoned wisps (default: 1h threshold)
+  bd mol wisp gc                # Clean abandoned wisps (default: 1h threshold)
-  bd wisp gc --dry-run      # Preview what would be cleaned
+  bd mol wisp gc --dry-run      # Preview what would be cleaned
-  bd wisp gc --age 24h      # Custom age threshold
+  bd mol wisp gc --age 24h      # Custom age threshold
-  bd wisp gc --all          # Also clean closed wisps older than threshold`,
+  bd mol wisp gc --all          # Also clean closed wisps older than threshold`,
 	Run: runWispGC,
 }
 
@@ -532,17 +554,17 @@ func runWispGC(cmd *cobra.Command, args []string) {
 	if store == nil {
 		if daemonClient != nil {
 			fmt.Fprintf(os.Stderr, "Error: wisp gc requires direct database access\n")
-			fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon wisp gc\n")
+			fmt.Fprintf(os.Stderr, "Hint: use --no-daemon flag: bd --no-daemon mol wisp gc\n")
 		} else {
 			fmt.Fprintf(os.Stderr, "Error: no database connection\n")
 		}
 		os.Exit(1)
 	}
 
-	// Query wisps from main database using Wisp filter
+	// Query wisps from main database using Ephemeral filter
-	wispFlag := true
+	ephemeralFlag := true
 	filter := types.IssueFilter{
-		Wisp: &wispFlag,
+		Ephemeral: &ephemeralFlag,
 	}
 	issues, err := store.SearchIssues(ctx, "", filter)
 	if err != nil {
@@ -634,7 +656,11 @@ func runWispGC(cmd *cobra.Command, args []string) {
 }
 
 func init() {
-	// Wisp create command flags
+	// Wisp command flags (for direct create: bd mol wisp <proto>)
+	wispCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)")
+	wispCmd.Flags().Bool("dry-run", false, "Preview what would be created")
+
+	// Wisp create command flags (kept for backwards compat: bd mol wisp create <proto>)
 	wispCreateCmd.Flags().StringSlice("var", []string{}, "Variable substitution (key=value)")
 	wispCreateCmd.Flags().Bool("dry-run", false, "Preview what would be created")
 
@@ -647,5 +673,5 @@ func init() {
 	wispCmd.AddCommand(wispCreateCmd)
 	wispCmd.AddCommand(wispListCmd)
 	wispCmd.AddCommand(wispGCCmd)
-	rootCmd.AddCommand(wispCmd)
+	molCmd.AddCommand(wispCmd)
 }

docs/ARCHITECTURE.md

@@ -275,7 +275,7 @@ open ──▶ in_progress ──▶ closed
 
 ```
 ┌─────────────────┐    ┌─────────────────┐    ┌─────────────────┐
-│ bd wisp create  │───▶│  Wisp Issues    │───▶│  bd mol squash  │
+│   bd mol wisp       │───▶│  Wisp Issues    │───▶│  bd mol squash  │
 │ (from template) │    │  (local-only)   │    │  (→ digest)     │
 └─────────────────┘    └─────────────────┘    └─────────────────┘
 ```

docs/CLI_REFERENCE.md

@@ -350,8 +350,8 @@ Beads uses a chemistry metaphor for template-based workflows. See [MOLECULES.md]
 | Phase | State | Storage | Command |
 |-------|-------|---------|---------|
 | Solid | Proto | `.beads/` | `bd mol catalog` |
-| Liquid | Mol | `.beads/` | `bd pour` |
+| Liquid | Mol | `.beads/` | `bd mol pour` |
-| Vapor | Wisp | `.beads/` (Wisp=true, not exported) | `bd wisp create` |
+| Vapor | Wisp | `.beads/` (Ephemeral=true, not exported) | `bd mol wisp` |
 
 ### Proto/Template Commands
 
@@ -370,32 +370,32 @@ bd mol distill <epic-id> --json
 
 ```bash
 # Instantiate proto as persistent mol (solid → liquid)
-bd pour <proto-id> --var key=value --json
+bd mol pour <proto-id> --var key=value --json
 
 # Preview what would be created
-bd pour <proto-id> --var key=value --dry-run
+bd mol pour <proto-id> --var key=value --dry-run
 
 # Assign root issue
-bd pour <proto-id> --var key=value --assignee alice --json
+bd mol pour <proto-id> --var key=value --assignee alice --json
 
 # Attach additional protos during pour
-bd pour <proto-id> --attach <other-proto> --json
+bd mol pour <proto-id> --attach <other-proto> --json
 ```
 
 ### Wisp Commands
 
 ```bash
 # Instantiate proto as ephemeral wisp (solid → vapor)
-bd wisp create <proto-id> --var key=value --json
+bd mol wisp <proto-id> --var key=value --json
 
 # List all wisps
-bd wisp list --json
+bd mol wisp list --json
-bd wisp list --all --json    # Include closed
+bd mol wisp list --all --json    # Include closed
 
 # Garbage collect orphaned wisps
-bd wisp gc --json
+bd mol wisp gc --json
-bd wisp gc --age 24h --json  # Custom age threshold
+bd mol wisp gc --age 24h --json  # Custom age threshold
-bd wisp gc --dry-run         # Preview what would be cleaned
+bd mol wisp gc --dry-run         # Preview what would be cleaned
 ```
 
 ### Bonding (Combining Work)
@@ -424,29 +424,29 @@ bd mol bond <A> <B> --dry-run
 
 ```bash
 # Compress wisp to permanent digest
-bd mol squash <wisp-id> --json
+bd mol squash <ephemeral-id> --json
 
 # With agent-provided summary
-bd mol squash <wisp-id> --summary "Work completed" --json
+bd mol squash <ephemeral-id> --summary "Work completed" --json
 
 # Preview
-bd mol squash <wisp-id> --dry-run
+bd mol squash <ephemeral-id> --dry-run
 
 # Keep wisp children after squash
-bd mol squash <wisp-id> --keep-children --json
+bd mol squash <ephemeral-id> --keep-children --json
 ```
 
 ### Burn (Discard Wisp)
 
 ```bash
 # Delete wisp without digest (destructive)
-bd mol burn <wisp-id> --json
+bd mol burn <ephemeral-id> --json
 
 # Preview
-bd mol burn <wisp-id> --dry-run
+bd mol burn <ephemeral-id> --dry-run
 
 # Skip confirmation
-bd mol burn <wisp-id> --force --json
+bd mol burn <ephemeral-id> --force --json
 ```
 
 **Note:** Most mol commands require `--no-daemon` flag when daemon is running.

docs/DELETIONS.md

@@ -202,7 +202,7 @@ The 1-hour grace period ensures tombstones propagate even with minor clock drift
 
 ## Wisps: Intentional Tombstone Bypass
 
-**Wisps** (ephemeral issues created by `bd wisp create`) are intentionally excluded from tombstone tracking.
+**Wisps** (ephemeral issues created by `bd mol wisp`) are intentionally excluded from tombstone tracking.
 
 ### Why Wisps Don't Need Tombstones
 

docs/MOLECULES.md

@@ -128,8 +128,8 @@ For reusable workflows, beads uses a chemistry metaphor:
 ### Phase Commands
 
 ```bash
-bd pour <proto>                  # Proto → Mol (persistent instance)
+bd mol pour <proto>              # Proto → Mol (persistent instance)
-bd wisp create <proto>           # Proto → Wisp (ephemeral instance)
+bd mol wisp <proto>              # Proto → Wisp (ephemeral instance)
 bd mol squash <id>               # Mol/Wisp → Digest (permanent record)
 bd mol burn <id>                 # Wisp → nothing (discard)
 ```
@@ -227,10 +227,10 @@ bd close <id> --reason "Done"
 Wisps accumulate if not squashed/burned:
 
 ```bash
-bd wisp list           # Check for orphans
+bd mol wisp list        # Check for orphans
-bd mol squash <id>     # Create digest
+bd mol squash <id>      # Create digest
-bd mol burn <id>       # Or discard
+bd mol burn <id>        # Or discard
-bd wisp gc             # Garbage collect old wisps
+bd mol wisp gc          # Garbage collect old wisps
 ```
 
 ## Layer Cake Architecture
@@ -272,8 +272,8 @@ bd dep tree <id>                 # Show dependency tree
 ### Molecules
 
 ```bash
-bd pour <proto> --var k=v        # Template → persistent mol
+bd mol pour <proto> --var k=v    # Template → persistent mol
-bd wisp create <proto>           # Template → ephemeral wisp
+bd mol wisp <proto>              # Template → ephemeral wisp
 bd mol bond A B                  # Connect work graphs
 bd mol squash <id>               # Compress to digest
 bd mol burn <id>                 # Discard without record

internal/routing/routes.go

@@ -67,6 +67,49 @@ func ExtractPrefix(id string) string {
 	return id[:idx+1] // Include the hyphen
 }
 
+// ExtractProjectFromPath extracts the project name from a route path.
+// For "beads/mayor/rig", returns "beads".
+// For "gastown/crew/max", returns "gastown".
+func ExtractProjectFromPath(path string) string {
+	// Get the first component of the path
+	parts := strings.Split(path, "/")
+	if len(parts) > 0 && parts[0] != "" {
+		return parts[0]
+	}
+	return ""
+}
+
+// ResolveToExternalRef attempts to convert a foreign issue ID to an external reference
+// using routes.jsonl for prefix-based routing.
+//
+// If the ID's prefix matches a route, returns "external:<project>:<id>".
+// Otherwise, returns empty string (no route found).
+//
+// Example: If routes.jsonl has {"prefix": "bd-", "path": "beads/mayor/rig"}
+// then ResolveToExternalRef("bd-abc", beadsDir) returns "external:beads:bd-abc"
+func ResolveToExternalRef(id, beadsDir string) string {
+	routes, err := LoadRoutes(beadsDir)
+	if err != nil || len(routes) == 0 {
+		return ""
+	}
+
+	prefix := ExtractPrefix(id)
+	if prefix == "" {
+		return ""
+	}
+
+	for _, route := range routes {
+		if route.Prefix == prefix {
+			project := ExtractProjectFromPath(route.Path)
+			if project != "" {
+				return fmt.Sprintf("external:%s:%s", project, id)
+			}
+		}
+	}
+
+	return ""
+}
+
 // ResolveBeadsDirForID determines which beads directory contains the given issue ID.
 // It first checks the local beads directory, then consults routes.jsonl for prefix-based routing.
 //

internal/routing/routing_test.go

@@ -88,3 +88,57 @@ func TestDetectUserRole_Fallback(t *testing.T) {
 		t.Errorf("DetectUserRole() = %v, want %v (fallback)", role, Contributor)
 	}
 }
+
+func TestExtractPrefix(t *testing.T) {
+	tests := []struct {
+		id   string
+		want string
+	}{
+		{"gt-abc123", "gt-"},
+		{"bd-xyz", "bd-"},
+		{"hq-1234", "hq-"},
+		{"abc123", ""},     // No hyphen
+		{"", ""},           // Empty string
+		{"-abc", "-"},      // Starts with hyphen
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.id, func(t *testing.T) {
+			got := ExtractPrefix(tt.id)
+			if got != tt.want {
+				t.Errorf("ExtractPrefix(%q) = %q, want %q", tt.id, got, tt.want)
+			}
+		})
+	}
+}
+
+func TestExtractProjectFromPath(t *testing.T) {
+	tests := []struct {
+		path string
+		want string
+	}{
+		{"beads/mayor/rig", "beads"},
+		{"gastown/crew/max", "gastown"},
+		{"simple", "simple"},
+		{"", ""},
+		{"/absolute/path", ""}, // Starts with /, first component is empty
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.path, func(t *testing.T) {
+			got := ExtractProjectFromPath(tt.path)
+			if got != tt.want {
+				t.Errorf("ExtractProjectFromPath(%q) = %q, want %q", tt.path, got, tt.want)
+			}
+		})
+	}
+}
+
+func TestResolveToExternalRef(t *testing.T) {
+	// This test is limited since it requires a routes.jsonl file
+	// Just test that it returns empty string for nonexistent directory
+	got := ResolveToExternalRef("bd-abc", "/nonexistent/path")
+	if got != "" {
+		t.Errorf("ResolveToExternalRef() = %q, want empty string for nonexistent path", got)
+	}
+}

internal/rpc/protocol.go

@@ -89,11 +89,11 @@ type CreateArgs struct {
 	WaitsFor     string `json:"waits_for,omitempty"`      // Spawner issue ID to wait for
 	WaitsForGate string `json:"waits_for_gate,omitempty"` // Gate type: all-children or any-children
 	// Messaging fields (bd-kwro)
-	Sender string `json:"sender,omitempty"` // Who sent this (for messages)
+	Sender    string `json:"sender,omitempty"`    // Who sent this (for messages)
-	Wisp   bool   `json:"wisp,omitempty"`   // Wisp = ephemeral vapor from the Steam Engine; bulk-deleted when closed
+	Ephemeral bool   `json:"ephemeral,omitempty"` // If true, not exported to JSONL; bulk-deleted when closed
 	RepliesTo string `json:"replies_to,omitempty"` // Issue ID for conversation threading
 	// ID generation (bd-hobo)
-	IDPrefix  string `json:"id_prefix,omitempty"`  // Override prefix for ID generation (mol, wisp, etc.)
+	IDPrefix  string `json:"id_prefix,omitempty"`  // Override prefix for ID generation (mol, eph, etc.)
 	CreatedBy string `json:"created_by,omitempty"` // Who created the issue
 }
 
@@ -115,8 +115,8 @@ type UpdateArgs struct {
 	RemoveLabels       []string `json:"remove_labels,omitempty"`
 	SetLabels          []string `json:"set_labels,omitempty"`
 	// Messaging fields (bd-kwro)
-	Sender *string `json:"sender,omitempty"` // Who sent this (for messages)
+	Sender    *string `json:"sender,omitempty"`    // Who sent this (for messages)
-	Wisp   *bool   `json:"wisp,omitempty"`   // Wisp = ephemeral vapor from the Steam Engine; bulk-deleted when closed
+	Ephemeral *bool   `json:"ephemeral,omitempty"` // If true, not exported to JSONL; bulk-deleted when closed
 	RepliesTo *string `json:"replies_to,omitempty"` // Issue ID for conversation threading
 	// Graph link fields (bd-fu83)
 	RelatesTo    *string `json:"relates_to,omitempty"`    // JSON array of related issue IDs
@@ -193,8 +193,8 @@ type ListArgs struct {
 	// Parent filtering (bd-yqhh)
 	ParentID string `json:"parent_id,omitempty"`
 
-	// Wisp filtering (bd-bkul)
+	// Ephemeral filtering (bd-bkul)
-	Wisp *bool `json:"wisp,omitempty"`
+	Ephemeral *bool `json:"ephemeral,omitempty"`
 }
 
 // CountArgs represents arguments for the count operation

internal/rpc/server_issues_epics.go

@@ -81,8 +81,8 @@ func updatesFromArgs(a UpdateArgs) map[string]interface{} {
 	if a.Sender != nil {
 		u["sender"] = *a.Sender
 	}
-	if a.Wisp != nil {
+	if a.Ephemeral != nil {
-		u["wisp"] = *a.Wisp
+		u["ephemeral"] = *a.Ephemeral
 	}
 	if a.RepliesTo != nil {
 		u["replies_to"] = *a.RepliesTo
@@ -176,8 +176,8 @@ func (s *Server) handleCreate(req *Request) Response {
 		EstimatedMinutes:   createArgs.EstimatedMinutes,
 		Status:             types.StatusOpen,
 		// Messaging fields (bd-kwro)
-		Sender: createArgs.Sender,
+		Sender:    createArgs.Sender,
-		Wisp:   createArgs.Wisp,
+		Ephemeral: createArgs.Ephemeral,
 		// NOTE: RepliesTo now handled via replies-to dependency (Decision 004)
 		// ID generation (bd-hobo)
 		IDPrefix:  createArgs.IDPrefix,
@@ -844,8 +844,8 @@ func (s *Server) handleList(req *Request) Response {
 		filter.ParentID = &listArgs.ParentID
 	}
 
-	// Wisp filtering (bd-bkul)
+	// Ephemeral filtering (bd-bkul)
-	filter.Wisp = listArgs.Wisp
+	filter.Ephemeral = listArgs.Ephemeral
 
 	// Guard against excessive ID lists to avoid SQLite parameter limits
 	const maxIDs = 1000
@@ -1480,7 +1480,7 @@ func (s *Server) handleGateCreate(req *Request) Response {
 		Status:    types.StatusOpen,
 		Priority:  1, // Gates are typically high priority
 		Assignee:  "deacon/",
-		Wisp:      true, // Gates are wisps (ephemeral)
+		Ephemeral:      true, // Gates are wisps (ephemeral)
 		AwaitType: args.AwaitType,
 		AwaitID:   args.AwaitID,
 		Timeout:   args.Timeout,

internal/storage/sqlite/dependencies.go

@@ -885,7 +885,7 @@ func (s *SQLiteStorage) scanIssues(ctx context.Context, rows *sql.Rows) ([]*type
 			issue.Sender = sender.String
 		}
 		if wisp.Valid && wisp.Int64 != 0 {
-			issue.Wisp = true
+			issue.Ephemeral = true
 		}
 		// Pinned field (bd-7h5)
 		if pinned.Valid && pinned.Int64 != 0 {
@@ -1006,7 +1006,7 @@ func (s *SQLiteStorage) scanIssuesWithDependencyType(ctx context.Context, rows *
 			issue.Sender = sender.String
 		}
 		if wisp.Valid && wisp.Int64 != 0 {
-			issue.Wisp = true
+			issue.Ephemeral = true
 		}
 		// Pinned field (bd-7h5)
 		if pinned.Valid && pinned.Int64 != 0 {

internal/storage/sqlite/graph_links_test.go

@@ -295,7 +295,7 @@ func TestRepliesTo(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Sender:      "alice",
 		Assignee:    "bob",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   time.Now(),
 		UpdatedAt:   time.Now(),
 	}
@@ -307,7 +307,7 @@ func TestRepliesTo(t *testing.T) {
 		IssueType:   types.TypeMessage,
 		Sender:      "bob",
 		Assignee:    "alice",
-		Wisp:        true,
+		Ephemeral:        true,
 		CreatedAt:   time.Now(),
 		UpdatedAt:   time.Now(),
 	}
@@ -363,7 +363,7 @@ func TestRepliesTo_Chain(t *testing.T) {
 			IssueType: types.TypeMessage,
 			Sender:    "user",
 			Assignee:  "inbox",
-			Wisp: true,
+			Ephemeral: true,
 			CreatedAt: time.Now(),
 			UpdatedAt: time.Now(),
 		}
@@ -415,7 +415,7 @@ func TestWispField(t *testing.T) {
 		Status:    types.StatusOpen,
 		Priority:  2,
 		IssueType: types.TypeMessage,
-		Wisp:      true,
+		Ephemeral:      true,
 		CreatedAt: time.Now(),
 		UpdatedAt: time.Now(),
 	}
@@ -426,7 +426,7 @@ func TestWispField(t *testing.T) {
 		Status:    types.StatusOpen,
 		Priority:  2,
 		IssueType: types.TypeTask,
-		Wisp:      false,
+		Ephemeral:      false,
 		CreatedAt: time.Now(),
 		UpdatedAt: time.Now(),
 	}
@@ -443,7 +443,7 @@ func TestWispField(t *testing.T) {
 	if err != nil {
 		t.Fatalf("GetIssue failed: %v", err)
 	}
-	if !savedWisp.Wisp {
+	if !savedWisp.Ephemeral {
 		t.Error("Wisp issue should have Wisp=true")
 	}
 
@@ -451,7 +451,7 @@ func TestWispField(t *testing.T) {
 	if err != nil {
 		t.Fatalf("GetIssue failed: %v", err)
 	}
-	if savedPermanent.Wisp {
+	if savedPermanent.Ephemeral {
 		t.Error("Permanent issue should have Wisp=false")
 	}
 }
@@ -468,7 +468,7 @@ func TestWispFilter(t *testing.T) {
 			Status:    types.StatusClosed, // Closed for cleanup test
 			Priority:  2,
 			IssueType: types.TypeMessage,
-			Wisp:      true,
+			Ephemeral:      true,
 			CreatedAt: time.Now(),
 			UpdatedAt: time.Now(),
 		}
@@ -483,7 +483,7 @@ func TestWispFilter(t *testing.T) {
 			Status:    types.StatusClosed,
 			Priority:  2,
 			IssueType: types.TypeTask,
-			Wisp:      false,
+			Ephemeral:      false,
 			CreatedAt: time.Now(),
 			UpdatedAt: time.Now(),
 		}
@@ -497,7 +497,7 @@ func TestWispFilter(t *testing.T) {
 	closedStatus := types.StatusClosed
 	wispFilter := types.IssueFilter{
 		Status: &closedStatus,
-		Wisp:   &wispTrue,
+		Ephemeral:   &wispTrue,
 	}
 
 	wispIssues, err := store.SearchIssues(ctx, "", wispFilter)
@@ -512,7 +512,7 @@ func TestWispFilter(t *testing.T) {
 	wispFalse := false
 	nonWispFilter := types.IssueFilter{
 		Status: &closedStatus,
-		Wisp:   &wispFalse,
+		Ephemeral:   &wispFalse,
 	}
 
 	permanentIssues, err := store.SearchIssues(ctx, "", nonWispFilter)

internal/storage/sqlite/issues.go

@@ -28,7 +28,7 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 	}
 
 	wisp := 0
-	if issue.Wisp {
+	if issue.Ephemeral {
 		wisp = 1
 	}
 	pinned := 0
@@ -94,7 +94,7 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 		}
 
 		wisp := 0
-		if issue.Wisp {
+		if issue.Ephemeral {
 			wisp = 1
 		}
 		pinned := 0

internal/storage/sqlite/migrations/028_tombstone_closed_at.go

@@ -3,6 +3,7 @@ package migrations
 import (
 	"database/sql"
 	"fmt"
+	"strings"
 )
 
 // MigrateTombstoneClosedAt updates the closed_at constraint to allow tombstones
@@ -22,8 +23,20 @@ func MigrateTombstoneClosedAt(db *sql.DB) error {
 	// SQLite doesn't support ALTER TABLE to modify CHECK constraints
 	// We must recreate the table with the new constraint
 
+	// Idempotency check: see if the new CHECK constraint already exists
+	// The new constraint contains "status = 'tombstone'" which the old one didn't
+	var tableSql string
+	err := db.QueryRow(`SELECT sql FROM sqlite_master WHERE type='table' AND name='issues'`).Scan(&tableSql)
+	if err != nil {
+		return fmt.Errorf("failed to get issues table schema: %w", err)
+	}
+	// If the schema already has the tombstone clause, migration is already applied
+	if strings.Contains(tableSql, "status = 'tombstone'") || strings.Contains(tableSql, `status = "tombstone"`) {
+		return nil
+	}
+
 	// Step 0: Drop views that depend on the issues table
-	_, err := db.Exec(`DROP VIEW IF EXISTS ready_issues`)
+	_, err = db.Exec(`DROP VIEW IF EXISTS ready_issues`)
 	if err != nil {
 		return fmt.Errorf("failed to drop ready_issues view: %w", err)
 	}
@@ -48,6 +61,7 @@ func MigrateTombstoneClosedAt(db *sql.DB) error {
 			assignee TEXT,
 			estimated_minutes INTEGER,
 			created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+			created_by TEXT DEFAULT '',
 			updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
 			closed_at DATETIME,
 			external_ref TEXT,
@@ -81,20 +95,73 @@ func MigrateTombstoneClosedAt(db *sql.DB) error {
 	}
 
 	// Step 2: Copy data from old table to new table
-	// List all columns explicitly to handle cases where old table has fewer columns
+	// We need to check if created_by column exists in the old table
-	// Note: created_by is added in migration 029, so don't reference it here
+	// If not, we insert a default empty string for it
-	_, err = db.Exec(`
+	var hasCreatedBy bool
-		INSERT INTO issues_new
+	rows, err := db.Query(`PRAGMA table_info(issues)`)
-		SELECT
+	if err != nil {
-			id, content_hash, title, description, design, acceptance_criteria, notes,
+		return fmt.Errorf("failed to get table info: %w", err)
-			status, priority, issue_type, assignee, estimated_minutes,
+	}
-			created_at, updated_at, closed_at, external_ref,
+	for rows.Next() {
-			source_repo, compaction_level, compacted_at, compacted_at_commit, original_size,
+		var cid int
-			deleted_at, deleted_by, delete_reason, original_type,
+		var name, ctype string
-			sender, ephemeral, close_reason, pinned, is_template,
+		var notnull, pk int
-			await_type, await_id, timeout_ns, waiters
+		var dflt interface{}
-		FROM issues
+		if err := rows.Scan(&cid, &name, &ctype, &notnull, &dflt, &pk); err != nil {
-	`)
+			rows.Close()
+			return fmt.Errorf("failed to scan table info: %w", err)
+		}
+		if name == "created_by" {
+			hasCreatedBy = true
+			break
+		}
+	}
+	rows.Close()
+
+	var insertSQL string
+	if hasCreatedBy {
+		// Old table has created_by, copy all columns directly
+		insertSQL = `
+			INSERT INTO issues_new (
+				id, content_hash, title, description, design, acceptance_criteria, notes,
+				status, priority, issue_type, assignee, estimated_minutes, created_at,
+				created_by, updated_at, closed_at, external_ref, source_repo, compaction_level,
+				compacted_at, compacted_at_commit, original_size, deleted_at, deleted_by,
+				delete_reason, original_type, sender, ephemeral, close_reason, pinned,
+				is_template, await_type, await_id, timeout_ns, waiters
+			)
+			SELECT
+				id, content_hash, title, description, design, acceptance_criteria, notes,
+				status, priority, issue_type, assignee, estimated_minutes, created_at,
+				created_by, updated_at, closed_at, external_ref, source_repo, compaction_level,
+				compacted_at, compacted_at_commit, original_size, deleted_at, deleted_by,
+				delete_reason, original_type, sender, ephemeral, close_reason, pinned,
+				is_template, await_type, await_id, timeout_ns, waiters
+			FROM issues
+		`
+	} else {
+		// Old table doesn't have created_by, use empty string default
+		insertSQL = `
+			INSERT INTO issues_new (
+				id, content_hash, title, description, design, acceptance_criteria, notes,
+				status, priority, issue_type, assignee, estimated_minutes, created_at,
+				created_by, updated_at, closed_at, external_ref, source_repo, compaction_level,
+				compacted_at, compacted_at_commit, original_size, deleted_at, deleted_by,
+				delete_reason, original_type, sender, ephemeral, close_reason, pinned,
+				is_template, await_type, await_id, timeout_ns, waiters
+			)
+			SELECT
+				id, content_hash, title, description, design, acceptance_criteria, notes,
+				status, priority, issue_type, assignee, estimated_minutes, created_at,
+				'', updated_at, closed_at, external_ref, source_repo, compaction_level,
+				compacted_at, compacted_at_commit, original_size, deleted_at, deleted_by,
+				delete_reason, original_type, sender, ephemeral, close_reason, pinned,
+				is_template, await_type, await_id, timeout_ns, waiters
+			FROM issues
+		`
+	}
+
+	_, err = db.Exec(insertSQL)
 	if err != nil {
 		return fmt.Errorf("failed to copy issues data: %w", err)
 	}

internal/storage/sqlite/multirepo.go

@@ -282,7 +282,7 @@ func (s *SQLiteStorage) upsertIssueInTx(ctx context.Context, tx *sql.Tx, issue *
 	err := tx.QueryRowContext(ctx, `SELECT id FROM issues WHERE id = ?`, issue.ID).Scan(&existingID)
 
 	wisp := 0
-	if issue.Wisp {
+	if issue.Ephemeral {
 		wisp = 1
 	}
 	pinned := 0

internal/storage/sqlite/multirepo_export.go

@@ -54,7 +54,7 @@ func (s *SQLiteStorage) ExportToMultiRepo(ctx context.Context) (map[string]int,
 	// Wisps exist only in SQLite and are shared via .beads/redirect, not JSONL.
 	filtered := make([]*types.Issue, 0, len(allIssues))
 	for _, issue := range allIssues {
-		if !issue.Wisp {
+		if !issue.Ephemeral {
 			filtered = append(filtered, issue)
 		}
 	}

internal/storage/sqlite/multirepo_test.go

@@ -909,7 +909,7 @@ func TestUpsertPreservesGateFields(t *testing.T) {
 		Status:    types.StatusOpen,
 		Priority:  1,
 		IssueType: types.TypeGate,
-		Wisp:      true,
+		Ephemeral: true,
 		AwaitType: "gh:run",
 		AwaitID:   "123456789",
 		Timeout:   30 * 60 * 1000000000, // 30 minutes in nanoseconds

internal/storage/sqlite/queries.go

@@ -349,7 +349,7 @@ func (s *SQLiteStorage) GetIssue(ctx context.Context, id string) (*types.Issue,
 		issue.Sender = sender.String
 	}
 	if wisp.Valid && wisp.Int64 != 0 {
-		issue.Wisp = true
+		issue.Ephemeral = true
 	}
 	// Pinned field (bd-7h5)
 	if pinned.Valid && pinned.Int64 != 0 {
@@ -562,7 +562,7 @@ func (s *SQLiteStorage) GetIssueByExternalRef(ctx context.Context, externalRef s
 		issue.Sender = sender.String
 	}
 	if wisp.Valid && wisp.Int64 != 0 {
-		issue.Wisp = true
+		issue.Ephemeral = true
 	}
 	// Pinned field (bd-7h5)
 	if pinned.Valid && pinned.Int64 != 0 {
@@ -1652,8 +1652,8 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 	}
 
 	// Wisp filtering (bd-kwro.9)
-	if filter.Wisp != nil {
+	if filter.Ephemeral != nil {
-		if *filter.Wisp {
+		if *filter.Ephemeral {
 			whereClauses = append(whereClauses, "ephemeral = 1") // SQL column is still 'ephemeral'
 		} else {
 			whereClauses = append(whereClauses, "(ephemeral = 0 OR ephemeral IS NULL)")

internal/storage/sqlite/ready.go

@@ -17,7 +17,8 @@ import (
 // Excludes pinned issues which are persistent anchors, not actionable work (bd-92u)
 func (s *SQLiteStorage) GetReadyWork(ctx context.Context, filter types.WorkFilter) ([]*types.Issue, error) {
 	whereClauses := []string{
-		"i.pinned = 0", // Exclude pinned issues (bd-92u)
+		"i.pinned = 0",                           // Exclude pinned issues (bd-92u)
+		"(i.ephemeral = 0 OR i.ephemeral IS NULL)", // Exclude wisps (hq-t15s)
 	}
 	args := []interface{}{}
 
@@ -399,7 +400,7 @@ func (s *SQLiteStorage) GetStaleIssues(ctx context.Context, filter types.StaleFi
 			issue.Sender = sender.String
 		}
 		if ephemeral.Valid && ephemeral.Int64 != 0 {
-			issue.Wisp = true
+			issue.Ephemeral = true
 		}
 		// Pinned field (bd-7h5)
 		if pinned.Valid && pinned.Int64 != 0 {

internal/storage/sqlite/schema.go

@@ -230,6 +230,7 @@ WITH RECURSIVE
 SELECT i.*
 FROM issues i
 WHERE i.status = 'open'
+  AND (i.ephemeral = 0 OR i.ephemeral IS NULL)
   AND NOT EXISTS (
     SELECT 1 FROM blocked_transitively WHERE issue_id = i.id
   );

internal/storage/sqlite/transaction.go

@@ -1089,8 +1089,8 @@ func (t *sqliteTxStorage) SearchIssues(ctx context.Context, query string, filter
 	}
 
 	// Wisp filtering (bd-kwro.9)
-	if filter.Wisp != nil {
+	if filter.Ephemeral != nil {
-		if *filter.Wisp {
+		if *filter.Ephemeral {
 			whereClauses = append(whereClauses, "ephemeral = 1") // SQL column is still 'ephemeral'
 		} else {
 			whereClauses = append(whereClauses, "(ephemeral = 0 OR ephemeral IS NULL)")
@@ -1244,7 +1244,7 @@ func scanIssueRow(row scanner) (*types.Issue, error) {
 		issue.Sender = sender.String
 	}
 	if wisp.Valid && wisp.Int64 != 0 {
-		issue.Wisp = true
+		issue.Ephemeral = true
 	}
 	// Pinned field (bd-7h5)
 	if pinned.Valid && pinned.Int64 != 0 {

internal/types/types.go

@@ -44,8 +44,8 @@ type Issue struct {
 	OriginalType string     `json:"original_type,omitempty"` // Issue type before deletion (for tombstones)
 
 	// Messaging fields (bd-kwro): inter-agent communication support
-	Sender string `json:"sender,omitempty"` // Who sent this (for messages)
+	Sender    string `json:"sender,omitempty"`    // Who sent this (for messages)
-	Wisp   bool   `json:"wisp,omitempty"`   // Wisp = ephemeral vapor from the Steam Engine; bulk-deleted when closed
+	Ephemeral bool   `json:"ephemeral,omitempty"` // If true, not exported to JSONL; bulk-deleted when closed
 	// NOTE: RepliesTo, RelatesTo, DuplicateOf, SupersededBy moved to dependencies table
 	// per Decision 004 (Edge Schema Consolidation). Use dependency API instead.
 
@@ -598,8 +598,8 @@ type IssueFilter struct {
 	// Tombstone filtering (bd-1bu)
 	IncludeTombstones bool // If false (default), exclude tombstones from results
 
-	// Wisp filtering (bd-kwro.9)
+	// Ephemeral filtering (bd-kwro.9)
-	Wisp *bool // Filter by wisp flag (nil = any, true = only wisps, false = only non-wisps)
+	Ephemeral *bool // Filter by ephemeral flag (nil = any, true = only ephemeral, false = only persistent)
 
 	// Pinned filtering (bd-7h5)
 	Pinned *bool // Filter by pinned flag (nil = any, true = only pinned, false = only non-pinned)

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 mol pour mol-feature                    # Shortcut for spawn --pour
-bd wisp create mol-patrol                  # Explicit wisp creation
+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 wisp 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 wisp list                    # List all wisps
+bd mol wisp list                     # List all wisps
-bd wisp list --json             # Machine-readable
+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 wisp 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 wisp 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 mol pour <proto>` | Shortcut for `spawn --pour` |
-| `bd wisp create <proto>` | Create ephemeral wisp |
+| `bd mol wisp <proto>` | Create ephemeral wisp |
-| `bd wisp list` | List all wisps |
+| `bd mol wisp list` | List all wisps |
-| `bd wisp gc` | Garbage collect orphaned 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 wisp 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