Fix daemon/direct mode inconsistency in graph commands (bd-fu83)

Commands relate, unrelate, duplicate, and supersede now properly
use RPC Update when daemonClient is available, instead of always
calling store.UpdateIssue() directly and bypassing the daemon.

Added RelatesTo, DuplicateOf, and SupersededBy fields to UpdateArgs
in the RPC protocol, and updated server_issues_epics.go to handle them.

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

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

cmd/bd/duplicate.go

@@ -112,14 +112,26 @@ func runDuplicate(cmd *cobra.Command, args []string) error {
 	}
 
 	// Update the duplicate issue with duplicate_of and close it
+	closedStatus := string(types.StatusClosed)
+	if daemonClient != nil {
+		// Use RPC for daemon mode (bd-fu83)
+		_, err := daemonClient.Update(&rpc.UpdateArgs{
+			ID:          duplicateID,
+			DuplicateOf: &canonicalID,
+			Status:      &closedStatus,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to mark as duplicate: %w", err)
+		}
+	} else {
 		updates := map[string]interface{}{
 			"duplicate_of": canonicalID,
-		"status":       string(types.StatusClosed),
+			"status":       closedStatus,
 		}
-
 		if err := store.UpdateIssue(ctx, duplicateID, updates, actor); err != nil {
 			return fmt.Errorf("failed to mark as duplicate: %w", err)
 		}
+	}
 
 	// Trigger auto-flush
 	if flushManager != nil {
@@ -199,14 +211,26 @@ func runSupersede(cmd *cobra.Command, args []string) error {
 	}
 
 	// Update the old issue with superseded_by and close it
+	closedStatus := string(types.StatusClosed)
+	if daemonClient != nil {
+		// Use RPC for daemon mode (bd-fu83)
+		_, err := daemonClient.Update(&rpc.UpdateArgs{
+			ID:           oldID,
+			SupersededBy: &newID,
+			Status:       &closedStatus,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to mark as superseded: %w", err)
+		}
+	} else {
 		updates := map[string]interface{}{
 			"superseded_by": newID,
-		"status":        string(types.StatusClosed),
+			"status":        closedStatus,
 		}
-
 		if err := store.UpdateIssue(ctx, oldID, updates, actor); err != nil {
 			return fmt.Errorf("failed to mark as superseded: %w", err)
 		}
+	}
 
 	// Trigger auto-flush
 	if flushManager != nil {

cmd/bd/relate.go

@@ -122,22 +122,46 @@ func runRelate(cmd *cobra.Command, args []string) error {
 	// Add id2 to issue1's relates_to if not already present
 	if !contains(issue1.RelatesTo, id2) {
 		newRelatesTo1 := append(issue1.RelatesTo, id2)
+		formattedRelatesTo1 := formatRelatesTo(newRelatesTo1)
+		if daemonClient != nil {
+			// Use RPC for daemon mode (bd-fu83)
+			_, err := daemonClient.Update(&rpc.UpdateArgs{
+				ID:        id1,
+				RelatesTo: &formattedRelatesTo1,
+			})
+			if err != nil {
+				return fmt.Errorf("failed to update %s: %w", id1, err)
+			}
+		} else {
 			if err := store.UpdateIssue(ctx, id1, map[string]interface{}{
-			"relates_to": formatRelatesTo(newRelatesTo1),
+				"relates_to": formattedRelatesTo1,
 			}, actor); err != nil {
 				return fmt.Errorf("failed to update %s: %w", id1, err)
 			}
 		}
+	}
 
 	// Add id1 to issue2's relates_to if not already present
 	if !contains(issue2.RelatesTo, id1) {
 		newRelatesTo2 := append(issue2.RelatesTo, id1)
+		formattedRelatesTo2 := formatRelatesTo(newRelatesTo2)
+		if daemonClient != nil {
+			// Use RPC for daemon mode (bd-fu83)
+			_, err := daemonClient.Update(&rpc.UpdateArgs{
+				ID:        id2,
+				RelatesTo: &formattedRelatesTo2,
+			})
+			if err != nil {
+				return fmt.Errorf("failed to update %s: %w", id2, err)
+			}
+		} else {
 			if err := store.UpdateIssue(ctx, id2, map[string]interface{}{
-			"relates_to": formatRelatesTo(newRelatesTo2),
+				"relates_to": formattedRelatesTo2,
 			}, actor); err != nil {
 				return fmt.Errorf("failed to update %s: %w", id2, err)
 			}
 		}
+	}
 
 	// Trigger auto-flush
 	if flushManager != nil {
@@ -232,19 +256,43 @@ func runUnrelate(cmd *cobra.Command, args []string) error {
 
 	// Remove id2 from issue1's relates_to
 	newRelatesTo1 := remove(issue1.RelatesTo, id2)
+	formattedRelatesTo1 := formatRelatesTo(newRelatesTo1)
+	if daemonClient != nil {
+		// Use RPC for daemon mode (bd-fu83)
+		_, err := daemonClient.Update(&rpc.UpdateArgs{
+			ID:        id1,
+			RelatesTo: &formattedRelatesTo1,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to update %s: %w", id1, err)
+		}
+	} else {
 		if err := store.UpdateIssue(ctx, id1, map[string]interface{}{
-		"relates_to": formatRelatesTo(newRelatesTo1),
+			"relates_to": formattedRelatesTo1,
 		}, actor); err != nil {
 			return fmt.Errorf("failed to update %s: %w", id1, err)
 		}
+	}
 
 	// Remove id1 from issue2's relates_to
 	newRelatesTo2 := remove(issue2.RelatesTo, id1)
+	formattedRelatesTo2 := formatRelatesTo(newRelatesTo2)
+	if daemonClient != nil {
+		// Use RPC for daemon mode (bd-fu83)
+		_, err := daemonClient.Update(&rpc.UpdateArgs{
+			ID:        id2,
+			RelatesTo: &formattedRelatesTo2,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to update %s: %w", id2, err)
+		}
+	} else {
 		if err := store.UpdateIssue(ctx, id2, map[string]interface{}{
-		"relates_to": formatRelatesTo(newRelatesTo2),
+			"relates_to": formattedRelatesTo2,
 		}, actor); err != nil {
 			return fmt.Errorf("failed to update %s: %w", id2, err)
 		}
+	}
 
 	// Trigger auto-flush
 	if flushManager != nil {

internal/rpc/protocol.go

@@ -99,6 +99,10 @@ type UpdateArgs struct {
 	Sender    *string `json:"sender,omitempty"`     // Who sent this (for messages)
 	Ephemeral *bool   `json:"ephemeral,omitempty"`  // Can be 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
+	DuplicateOf  *string `json:"duplicate_of,omitempty"`  // Canonical issue ID if duplicate
+	SupersededBy *string `json:"superseded_by,omitempty"` // Replacement issue ID if obsolete
 }
 
 // CloseArgs represents arguments for the close operation

internal/rpc/server_issues_epics.go

@@ -87,6 +87,16 @@ func updatesFromArgs(a UpdateArgs) map[string]interface{} {
 	if a.RepliesTo != nil {
 		u["replies_to"] = *a.RepliesTo
 	}
+	// Graph link fields (bd-fu83)
+	if a.RelatesTo != nil {
+		u["relates_to"] = *a.RelatesTo
+	}
+	if a.DuplicateOf != nil {
+		u["duplicate_of"] = *a.DuplicateOf
+	}
+	if a.SupersededBy != nil {
+		u["superseded_by"] = *a.SupersededBy
+	}
 	return u
 }