feat: add graph links and hooks system (bd-kwro.2-5, bd-kwro.8)

- bd mail reply: reply to messages with thread linking via replies_to
- bd show --thread: display full conversation threads
- bd relate/unrelate: bidirectional relates_to links for knowledge graph
- bd duplicate --of: mark issues as duplicates with auto-close
- bd supersede --with: mark issues as superseded with auto-close
- Hooks system: on_create, on_update, on_close, on_message in .beads/hooks/
- RPC protocol: added Sender, Ephemeral, RepliesTo fields to CreateArgs/UpdateArgs

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

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

cmd/bd/create.go

@@ -10,6 +10,7 @@ import (
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/debug"
+	"github.com/steveyegge/beads/internal/hooks"
 	"github.com/steveyegge/beads/internal/routing"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/types"
@@ -250,19 +251,22 @@ var createCmd = &cobra.Command{
 				FatalError("%v", err)
 			}
 
+			// Parse response to get issue for hook
+			var issue types.Issue
+			if err := json.Unmarshal(resp.Data, &issue); err != nil {
+				FatalError("parsing response: %v", err)
+			}
+
+			// Run create hook (bd-kwro.8)
+			if hookRunner != nil {
+				hookRunner.Run(hooks.EventCreate, &issue)
+			}
+
 			if jsonOutput {
 				fmt.Println(string(resp.Data))
 			} else if silent {
-				var issue types.Issue
-				if err := json.Unmarshal(resp.Data, &issue); err != nil {
-					FatalError("parsing response: %v", err)
-				}
 				fmt.Println(issue.ID)
 			} else {
-				var issue types.Issue
-				if err := json.Unmarshal(resp.Data, &issue); err != nil {
-					FatalError("parsing response: %v", err)
-				}
 				green := color.New(color.FgGreen).SprintFunc()
 				fmt.Printf("%s Created issue: %s\n", green("✓"), issue.ID)
 				fmt.Printf("  Title: %s\n", issue.Title)
@@ -393,6 +397,11 @@ var createCmd = &cobra.Command{
 		// Schedule auto-flush
 		markDirtyAndScheduleFlush()
 
+		// Run create hook (bd-kwro.8)
+		if hookRunner != nil {
+			hookRunner.Run(hooks.EventCreate, issue)
+		}
+
 		if jsonOutput {
 			outputJSON(issue)
 		} else if silent {

cmd/bd/duplicate.go

@@ -0,0 +1,230 @@
+package main
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+
+	"github.com/fatih/color"
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
+)
+
+var duplicateCmd = &cobra.Command{
+	Use:   "duplicate <id> --of <canonical>",
+	Short: "Mark an issue as a duplicate of another",
+	Long: `Mark an issue as a duplicate of a canonical issue.
+
+The duplicate issue is automatically closed with a reference to the canonical.
+This is essential for large issue databases with many similar reports.
+
+Examples:
+  bd duplicate bd-abc --of bd-xyz    # Mark bd-abc as duplicate of bd-xyz`,
+	Args: cobra.ExactArgs(1),
+	RunE: runDuplicate,
+}
+
+var supersedeCmd = &cobra.Command{
+	Use:   "supersede <id> --with <new>",
+	Short: "Mark an issue as superseded by a newer one",
+	Long: `Mark an issue as superseded by a newer version.
+
+The superseded issue is automatically closed with a reference to the replacement.
+Useful for design docs, specs, and evolving artifacts.
+
+Examples:
+  bd supersede bd-old --with bd-new    # Mark bd-old as superseded by bd-new`,
+	Args: cobra.ExactArgs(1),
+	RunE: runSupersede,
+}
+
+var (
+	duplicateOf    string
+	supersededWith string
+)
+
+func init() {
+	duplicateCmd.Flags().StringVar(&duplicateOf, "of", "", "Canonical issue ID (required)")
+	_ = duplicateCmd.MarkFlagRequired("of")
+	rootCmd.AddCommand(duplicateCmd)
+
+	supersedeCmd.Flags().StringVar(&supersededWith, "with", "", "Replacement issue ID (required)")
+	_ = supersedeCmd.MarkFlagRequired("with")
+	rootCmd.AddCommand(supersedeCmd)
+}
+
+func runDuplicate(cmd *cobra.Command, args []string) error {
+	CheckReadonly("duplicate")
+
+	ctx := rootCtx
+
+	// Resolve partial IDs
+	var duplicateID, canonicalID string
+	if daemonClient != nil {
+		resp1, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[0]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		if err := json.Unmarshal(resp1.Data, &duplicateID); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: duplicateOf})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", duplicateOf, err)
+		}
+		if err := json.Unmarshal(resp2.Data, &canonicalID); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		duplicateID, err = utils.ResolvePartialID(ctx, store, args[0])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		canonicalID, err = utils.ResolvePartialID(ctx, store, duplicateOf)
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", duplicateOf, err)
+		}
+	}
+
+	if duplicateID == canonicalID {
+		return fmt.Errorf("cannot mark an issue as duplicate of itself")
+	}
+
+	// Verify canonical issue exists
+	var canonical *types.Issue
+	if daemonClient != nil {
+		resp, err := daemonClient.Show(&rpc.ShowArgs{ID: canonicalID})
+		if err != nil {
+			return fmt.Errorf("canonical issue not found: %s", canonicalID)
+		}
+		if err := json.Unmarshal(resp.Data, &canonical); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		canonical, err = store.GetIssue(ctx, canonicalID)
+		if err != nil || canonical == nil {
+			return fmt.Errorf("canonical issue not found: %s", canonicalID)
+		}
+	}
+
+	// Update the duplicate issue with duplicate_of and close it
+	updates := map[string]interface{}{
+		"duplicate_of": canonicalID,
+		"status":       string(types.StatusClosed),
+	}
+
+	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 {
+		flushManager.MarkDirty(false)
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"duplicate":  duplicateID,
+			"canonical":  canonicalID,
+			"status":     "closed",
+		}
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		return encoder.Encode(result)
+	}
+
+	green := color.New(color.FgGreen).SprintFunc()
+	fmt.Printf("%s Marked %s as duplicate of %s (closed)\n", green("✓"), duplicateID, canonicalID)
+	return nil
+}
+
+func runSupersede(cmd *cobra.Command, args []string) error {
+	CheckReadonly("supersede")
+
+	ctx := rootCtx
+
+	// Resolve partial IDs
+	var oldID, newID string
+	if daemonClient != nil {
+		resp1, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[0]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		if err := json.Unmarshal(resp1.Data, &oldID); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: supersededWith})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", supersededWith, err)
+		}
+		if err := json.Unmarshal(resp2.Data, &newID); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		oldID, err = utils.ResolvePartialID(ctx, store, args[0])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		newID, err = utils.ResolvePartialID(ctx, store, supersededWith)
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", supersededWith, err)
+		}
+	}
+
+	if oldID == newID {
+		return fmt.Errorf("cannot mark an issue as superseded by itself")
+	}
+
+	// Verify new issue exists
+	var newIssue *types.Issue
+	if daemonClient != nil {
+		resp, err := daemonClient.Show(&rpc.ShowArgs{ID: newID})
+		if err != nil {
+			return fmt.Errorf("replacement issue not found: %s", newID)
+		}
+		if err := json.Unmarshal(resp.Data, &newIssue); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		newIssue, err = store.GetIssue(ctx, newID)
+		if err != nil || newIssue == nil {
+			return fmt.Errorf("replacement issue not found: %s", newID)
+		}
+	}
+
+	// Update the old issue with superseded_by and close it
+	updates := map[string]interface{}{
+		"superseded_by": newID,
+		"status":        string(types.StatusClosed),
+	}
+
+	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 {
+		flushManager.MarkDirty(false)
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"superseded":    oldID,
+			"replacement":   newID,
+			"status":        "closed",
+		}
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		return encoder.Encode(result)
+	}
+
+	green := color.New(color.FgGreen).SprintFunc()
+	fmt.Printf("%s Marked %s as superseded by %s (closed)\n", green("✓"), oldID, newID)
+	return nil
+}

cmd/bd/mail.go

@@ -9,6 +9,7 @@ import (
 
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/beads/internal/config"
+	"github.com/steveyegge/beads/internal/hooks"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -85,6 +86,21 @@ Examples:
 	RunE: runMailAck,
 }
 
+var mailReplyCmd = &cobra.Command{
+	Use:   "reply <id> -m <body>",
+	Short: "Reply to a message",
+	Long: `Reply to an existing message, creating a conversation thread.
+
+Creates a new message with replies_to set to the original message,
+and sends it to the original sender.
+
+Examples:
+  bd mail reply bd-abc123 -m "Thanks for the update!"
+  bd mail reply bd-abc123 -m "Done" --urgent`,
+	Args: cobra.ExactArgs(1),
+	RunE: runMailReply,
+}
+
 // Mail command flags
 var (
 	mailSubject      string
@@ -101,6 +117,7 @@ func init() {
 	mailCmd.AddCommand(mailInboxCmd)
 	mailCmd.AddCommand(mailReadCmd)
 	mailCmd.AddCommand(mailAckCmd)
+	mailCmd.AddCommand(mailReplyCmd)
 
 	// Send command flags
 	mailSendCmd.Flags().StringVarP(&mailSubject, "subject", "s", "", "Message subject (required)")
@@ -119,6 +136,12 @@ func init() {
 
 	// Ack command flags
 	mailAckCmd.Flags().StringVar(&mailIdentity, "identity", "", "Override identity")
+
+	// Reply command flags
+	mailReplyCmd.Flags().StringVarP(&mailBody, "body", "m", "", "Reply body (required)")
+	mailReplyCmd.Flags().BoolVar(&mailUrgent, "urgent", false, "Set priority=0 (urgent)")
+	mailReplyCmd.Flags().StringVar(&mailIdentity, "identity", "", "Override sender identity")
+	_ = mailReplyCmd.MarkFlagRequired("body")
 }
 
 func runMailSend(cmd *cobra.Command, args []string) error {
@@ -141,6 +164,8 @@ func runMailSend(cmd *cobra.Command, args []string) error {
 			IssueType:   string(types.TypeMessage),
 			Priority:    priority,
 			Assignee:    recipient,
+			Sender:      sender,
+			Ephemeral:   true, // Messages can be bulk-deleted
 		}
 
 		resp, err := daemonClient.Create(createArgs)
@@ -148,13 +173,17 @@ func runMailSend(cmd *cobra.Command, args []string) error {
 			return fmt.Errorf("failed to send message: %w", err)
 		}
 
-		// Parse response to get issue ID and update sender field
+		// Parse response to get issue ID
 		var issue types.Issue
 		if err := json.Unmarshal(resp.Data, &issue); err != nil {
 			return fmt.Errorf("parsing response: %w", err)
 		}
 
-		// Note: sender/ephemeral fields need daemon support - for now they work in direct mode
+		// Run message hook (bd-kwro.8)
+		if hookRunner != nil {
+			hookRunner.Run(hooks.EventMessage, &issue)
+		}
+
 		if jsonOutput {
 			result := map[string]interface{}{
 				"id":        issue.ID,
@@ -202,6 +231,11 @@ func runMailSend(cmd *cobra.Command, args []string) error {
 		flushManager.MarkDirty(false)
 	}
 
+	// Run message hook (bd-kwro.8)
+	if hookRunner != nil {
+		hookRunner.Run(hooks.EventMessage, issue)
+	}
+
 	if jsonOutput {
 		result := map[string]interface{}{
 			"id":        issue.ID,
@@ -487,3 +521,152 @@ func runMailAck(cmd *cobra.Command, args []string) error {
 
 	return nil
 }
+
+func runMailReply(cmd *cobra.Command, args []string) error {
+	CheckReadonly("mail reply")
+
+	messageID := args[0]
+	sender := config.GetIdentity(mailIdentity)
+
+	// Get the original message
+	var originalMsg *types.Issue
+
+	if daemonClient != nil {
+		resp, err := daemonClient.Show(&rpc.ShowArgs{ID: messageID})
+		if err != nil {
+			return fmt.Errorf("failed to get original message: %w", err)
+		}
+		if err := json.Unmarshal(resp.Data, &originalMsg); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		originalMsg, err = store.GetIssue(rootCtx, messageID)
+		if err != nil {
+			return fmt.Errorf("failed to get original message: %w", err)
+		}
+	}
+
+	if originalMsg == nil {
+		return fmt.Errorf("message not found: %s", messageID)
+	}
+
+	if originalMsg.IssueType != types.TypeMessage {
+		return fmt.Errorf("%s is not a message (type: %s)", messageID, originalMsg.IssueType)
+	}
+
+	// Determine recipient: reply goes to the original sender
+	recipient := originalMsg.Sender
+	if recipient == "" {
+		return fmt.Errorf("original message has no sender, cannot determine reply recipient")
+	}
+
+	// Build reply subject
+	subject := originalMsg.Title
+	if !strings.HasPrefix(strings.ToLower(subject), "re:") {
+		subject = "Re: " + subject
+	}
+
+	// Determine priority
+	priority := 2 // default: normal
+	if mailUrgent {
+		priority = 0
+	}
+
+	// Create the reply message
+	now := time.Now()
+	reply := &types.Issue{
+		Title:       subject,
+		Description: mailBody,
+		Status:      types.StatusOpen,
+		Priority:    priority,
+		IssueType:   types.TypeMessage,
+		Assignee:    recipient,
+		Sender:      sender,
+		Ephemeral:   true,
+		RepliesTo:   messageID, // Thread link
+		CreatedAt:   now,
+		UpdatedAt:   now,
+	}
+
+	if daemonClient != nil {
+		// Daemon mode - create reply with all messaging fields
+		createArgs := &rpc.CreateArgs{
+			Title:       reply.Title,
+			Description: reply.Description,
+			IssueType:   string(types.TypeMessage),
+			Priority:    priority,
+			Assignee:    recipient,
+			Sender:      sender,
+			Ephemeral:   true,
+			RepliesTo:   messageID, // Thread link
+		}
+
+		resp, err := daemonClient.Create(createArgs)
+		if err != nil {
+			return fmt.Errorf("failed to send reply: %w", err)
+		}
+
+		var createdIssue types.Issue
+		if err := json.Unmarshal(resp.Data, &createdIssue); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+
+		if jsonOutput {
+			result := map[string]interface{}{
+				"id":         createdIssue.ID,
+				"to":         recipient,
+				"from":       sender,
+				"subject":    subject,
+				"replies_to": messageID,
+				"priority":   priority,
+				"timestamp":  createdIssue.CreatedAt,
+			}
+			encoder := json.NewEncoder(os.Stdout)
+			encoder.SetIndent("", "  ")
+			return encoder.Encode(result)
+		}
+
+		fmt.Printf("Reply sent: %s\n", createdIssue.ID)
+		fmt.Printf("  To: %s\n", recipient)
+		fmt.Printf("  Re: %s\n", messageID)
+		if mailUrgent {
+			fmt.Printf("  Priority: URGENT\n")
+		}
+		return nil
+	}
+
+	// Direct mode
+	if err := store.CreateIssue(rootCtx, reply, actor); err != nil {
+		return fmt.Errorf("failed to send reply: %w", err)
+	}
+
+	// Trigger auto-flush
+	if flushManager != nil {
+		flushManager.MarkDirty(false)
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"id":         reply.ID,
+			"to":         recipient,
+			"from":       sender,
+			"subject":    subject,
+			"replies_to": messageID,
+			"priority":   priority,
+			"timestamp":  reply.CreatedAt,
+		}
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		return encoder.Encode(result)
+	}
+
+	fmt.Printf("Reply sent: %s\n", reply.ID)
+	fmt.Printf("  To: %s\n", recipient)
+	fmt.Printf("  Re: %s\n", messageID)
+	if mailUrgent {
+		fmt.Printf("  Priority: URGENT\n")
+	}
+
+	return nil
+}

cmd/bd/main.go

@@ -18,6 +18,7 @@ import (
 	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/debug"
+	"github.com/steveyegge/beads/internal/hooks"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/storage/memory"
@@ -83,6 +84,9 @@ var (
 	// Auto-flush manager (replaces timer-based approach to fix bd-52)
 	flushManager *FlushManager
 
+	// Hook runner for extensibility (bd-kwro.8)
+	hookRunner *hooks.Runner
+
 	// skipFinalFlush is set by sync command when sync.branch mode completes successfully.
 	// This prevents PersistentPostRun from re-exporting and dirtying the working directory.
 	skipFinalFlush = false
@@ -599,6 +603,13 @@ var rootCmd = &cobra.Command{
 			flushManager = NewFlushManager(autoFlushEnabled, getDebounceDuration())
 		}
 
+		// Initialize hook runner (bd-kwro.8)
+		// dbPath is .beads/something.db, so workspace root is parent of .beads
+		if dbPath != "" {
+			beadsDir := filepath.Dir(dbPath)
+			hookRunner = hooks.NewRunner(filepath.Join(beadsDir, "hooks"))
+		}
+
 		// Warn if multiple databases detected in directory hierarchy
 		warnMultipleDatabases(dbPath)
 

cmd/bd/relate.go

@@ -0,0 +1,295 @@
+package main
+
+import (
+	"encoding/json"
+	"fmt"
+	"os"
+
+	"github.com/fatih/color"
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/rpc"
+	"github.com/steveyegge/beads/internal/types"
+	"github.com/steveyegge/beads/internal/utils"
+)
+
+var relateCmd = &cobra.Command{
+	Use:   "relate <id1> <id2>",
+	Short: "Create a bidirectional relates_to link between issues",
+	Long: `Create a loose 'see also' relationship between two issues.
+
+The relates_to link is bidirectional - both issues will reference each other.
+This enables knowledge graph connections without blocking or hierarchy.
+
+Examples:
+  bd relate bd-abc bd-xyz    # Link two related issues
+  bd relate bd-123 bd-456    # Create see-also connection`,
+	Args: cobra.ExactArgs(2),
+	RunE: runRelate,
+}
+
+var unrelateCmd = &cobra.Command{
+	Use:   "unrelate <id1> <id2>",
+	Short: "Remove a relates_to link between issues",
+	Long: `Remove a relates_to relationship between two issues.
+
+Removes the link in both directions.
+
+Example:
+  bd unrelate bd-abc bd-xyz`,
+	Args: cobra.ExactArgs(2),
+	RunE: runUnrelate,
+}
+
+func init() {
+	rootCmd.AddCommand(relateCmd)
+	rootCmd.AddCommand(unrelateCmd)
+}
+
+func runRelate(cmd *cobra.Command, args []string) error {
+	CheckReadonly("relate")
+
+	ctx := rootCtx
+
+	// Resolve partial IDs
+	var id1, id2 string
+	if daemonClient != nil {
+		resp1, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[0]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		if err := json.Unmarshal(resp1.Data, &id1); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[1]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[1], err)
+		}
+		if err := json.Unmarshal(resp2.Data, &id2); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		id1, err = utils.ResolvePartialID(ctx, store, args[0])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		id2, err = utils.ResolvePartialID(ctx, store, args[1])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[1], err)
+		}
+	}
+
+	if id1 == id2 {
+		return fmt.Errorf("cannot relate an issue to itself")
+	}
+
+	// Get both issues
+	var issue1, issue2 *types.Issue
+	if daemonClient != nil {
+		resp1, err := daemonClient.Show(&rpc.ShowArgs{ID: id1})
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id1, err)
+		}
+		if err := json.Unmarshal(resp1.Data, &issue1); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.Show(&rpc.ShowArgs{ID: id2})
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id2, err)
+		}
+		if err := json.Unmarshal(resp2.Data, &issue2); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		issue1, err = store.GetIssue(ctx, id1)
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id1, err)
+		}
+		issue2, err = store.GetIssue(ctx, id2)
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id2, err)
+		}
+	}
+
+	if issue1 == nil {
+		return fmt.Errorf("issue not found: %s", id1)
+	}
+	if issue2 == nil {
+		return fmt.Errorf("issue not found: %s", id2)
+	}
+
+	// Add id2 to issue1's relates_to if not already present
+	if !contains(issue1.RelatesTo, id2) {
+		newRelatesTo1 := append(issue1.RelatesTo, id2)
+		if err := store.UpdateIssue(ctx, id1, map[string]interface{}{
+			"relates_to": formatRelatesTo(newRelatesTo1),
+		}, 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)
+		if err := store.UpdateIssue(ctx, id2, map[string]interface{}{
+			"relates_to": formatRelatesTo(newRelatesTo2),
+		}, actor); err != nil {
+			return fmt.Errorf("failed to update %s: %w", id2, err)
+		}
+	}
+
+	// Trigger auto-flush
+	if flushManager != nil {
+		flushManager.MarkDirty(false)
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"id1":     id1,
+			"id2":     id2,
+			"related": true,
+		}
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		return encoder.Encode(result)
+	}
+
+	green := color.New(color.FgGreen).SprintFunc()
+	fmt.Printf("%s Linked %s ↔ %s\n", green("✓"), id1, id2)
+	return nil
+}
+
+func runUnrelate(cmd *cobra.Command, args []string) error {
+	CheckReadonly("unrelate")
+
+	ctx := rootCtx
+
+	// Resolve partial IDs
+	var id1, id2 string
+	if daemonClient != nil {
+		resp1, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[0]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		if err := json.Unmarshal(resp1.Data, &id1); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.ResolveID(&rpc.ResolveIDArgs{ID: args[1]})
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[1], err)
+		}
+		if err := json.Unmarshal(resp2.Data, &id2); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		id1, err = utils.ResolvePartialID(ctx, store, args[0])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[0], err)
+		}
+		id2, err = utils.ResolvePartialID(ctx, store, args[1])
+		if err != nil {
+			return fmt.Errorf("failed to resolve %s: %w", args[1], err)
+		}
+	}
+
+	// Get both issues
+	var issue1, issue2 *types.Issue
+	if daemonClient != nil {
+		resp1, err := daemonClient.Show(&rpc.ShowArgs{ID: id1})
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id1, err)
+		}
+		if err := json.Unmarshal(resp1.Data, &issue1); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+		resp2, err := daemonClient.Show(&rpc.ShowArgs{ID: id2})
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id2, err)
+		}
+		if err := json.Unmarshal(resp2.Data, &issue2); err != nil {
+			return fmt.Errorf("parsing response: %w", err)
+		}
+	} else {
+		var err error
+		issue1, err = store.GetIssue(ctx, id1)
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id1, err)
+		}
+		issue2, err = store.GetIssue(ctx, id2)
+		if err != nil {
+			return fmt.Errorf("failed to get issue %s: %w", id2, err)
+		}
+	}
+
+	if issue1 == nil {
+		return fmt.Errorf("issue not found: %s", id1)
+	}
+	if issue2 == nil {
+		return fmt.Errorf("issue not found: %s", id2)
+	}
+
+	// Remove id2 from issue1's relates_to
+	newRelatesTo1 := remove(issue1.RelatesTo, id2)
+	if err := store.UpdateIssue(ctx, id1, map[string]interface{}{
+		"relates_to": formatRelatesTo(newRelatesTo1),
+	}, 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)
+	if err := store.UpdateIssue(ctx, id2, map[string]interface{}{
+		"relates_to": formatRelatesTo(newRelatesTo2),
+	}, actor); err != nil {
+		return fmt.Errorf("failed to update %s: %w", id2, err)
+	}
+
+	// Trigger auto-flush
+	if flushManager != nil {
+		flushManager.MarkDirty(false)
+	}
+
+	if jsonOutput {
+		result := map[string]interface{}{
+			"id1":       id1,
+			"id2":       id2,
+			"unrelated": true,
+		}
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		return encoder.Encode(result)
+	}
+
+	green := color.New(color.FgGreen).SprintFunc()
+	fmt.Printf("%s Unlinked %s ↔ %s\n", green("✓"), id1, id2)
+	return nil
+}
+
+func contains(slice []string, item string) bool {
+	for _, s := range slice {
+		if s == item {
+			return true
+		}
+	}
+	return false
+}
+
+func remove(slice []string, item string) []string {
+	result := make([]string, 0, len(slice))
+	for _, s := range slice {
+		if s != item {
+			result = append(result, s)
+		}
+	}
+	return result
+}
+
+func formatRelatesTo(ids []string) string {
+	if len(ids) == 0 {
+		return ""
+	}
+	data, _ := json.Marshal(ids)
+	return string(data)
+}

cmd/bd/show.go

@@ -1,14 +1,17 @@
 package main
 
 import (
+	"context"
 	"encoding/json"
 	"fmt"
 	"os"
 	"os/exec"
+	"sort"
 	"strings"
 
 	"github.com/fatih/color"
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/hooks"
 	"github.com/steveyegge/beads/internal/rpc"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
@@ -22,6 +25,7 @@ var showCmd = &cobra.Command{
 	Args:  cobra.MinimumNArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		jsonOutput, _ := cmd.Flags().GetBool("json")
+		showThread, _ := cmd.Flags().GetBool("thread")
 		ctx := rootCtx
 
 		// Check database freshness before reading (bd-2q6d, bd-c4rq)
@@ -61,6 +65,12 @@ var showCmd = &cobra.Command{
 			}
 		}
 
+		// Handle --thread flag: show full conversation thread
+		if showThread && len(resolvedIDs) > 0 {
+			showMessageThread(ctx, resolvedIDs[0], jsonOutput)
+			return
+		}
+
 		// If daemon is running, use RPC
 		if daemonClient != nil {
 			allDetails := []interface{}{}
@@ -637,12 +647,17 @@ var updateCmd = &cobra.Command{
 					continue
 				}
 
-				if jsonOutput {
-					var issue types.Issue
-					if err := json.Unmarshal(resp.Data, &issue); err == nil {
+				var issue types.Issue
+				if err := json.Unmarshal(resp.Data, &issue); err == nil {
+					// Run update hook (bd-kwro.8)
+					if hookRunner != nil {
+						hookRunner.Run(hooks.EventUpdate, &issue)
+					}
+					if jsonOutput {
 						updatedIssues = append(updatedIssues, &issue)
 					}
-				} else {
+				}
+				if !jsonOutput {
 					green := color.New(color.FgGreen).SprintFunc()
 					fmt.Printf("%s Updated issue: %s\n", green("✓"), id)
 				}
@@ -716,8 +731,13 @@ var updateCmd = &cobra.Command{
 				}
 			}
 
+			// Run update hook (bd-kwro.8)
+			issue, _ := store.GetIssue(ctx, id)
+			if issue != nil && hookRunner != nil {
+				hookRunner.Run(hooks.EventUpdate, issue)
+			}
+
 			if jsonOutput {
-				issue, _ := store.GetIssue(ctx, id)
 				if issue != nil {
 					updatedIssues = append(updatedIssues, issue)
 				}
@@ -990,12 +1010,17 @@ var closeCmd = &cobra.Command{
 					continue
 				}
 
-				if jsonOutput {
-					var issue types.Issue
-					if err := json.Unmarshal(resp.Data, &issue); err == nil {
+				var issue types.Issue
+				if err := json.Unmarshal(resp.Data, &issue); err == nil {
+					// Run close hook (bd-kwro.8)
+					if hookRunner != nil {
+						hookRunner.Run(hooks.EventClose, &issue)
+					}
+					if jsonOutput {
 						closedIssues = append(closedIssues, &issue)
 					}
-				} else {
+				}
+				if !jsonOutput {
 					green := color.New(color.FgGreen).SprintFunc()
 					fmt.Printf("%s Closed %s: %s\n", green("✓"), id, reason)
 				}
@@ -1014,8 +1039,14 @@ var closeCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error closing %s: %v\n", id, err)
 				continue
 			}
+
+			// Run close hook (bd-kwro.8)
+			issue, _ := store.GetIssue(ctx, id)
+			if issue != nil && hookRunner != nil {
+				hookRunner.Run(hooks.EventClose, issue)
+			}
+
 			if jsonOutput {
-				issue, _ := store.GetIssue(ctx, id)
 				if issue != nil {
 					closedIssues = append(closedIssues, issue)
 				}
@@ -1036,8 +1067,178 @@ var closeCmd = &cobra.Command{
 	},
 }
 
+// showMessageThread displays a full conversation thread for a message
+func showMessageThread(ctx context.Context, messageID string, jsonOutput bool) {
+	// Get the starting message
+	var startMsg *types.Issue
+	var err error
+
+	if daemonClient != nil {
+		resp, err := daemonClient.Show(&rpc.ShowArgs{ID: messageID})
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error fetching message %s: %v\n", messageID, err)
+			os.Exit(1)
+		}
+		if err := json.Unmarshal(resp.Data, &startMsg); err != nil {
+			fmt.Fprintf(os.Stderr, "Error parsing response: %v\n", err)
+			os.Exit(1)
+		}
+	} else {
+		startMsg, err = store.GetIssue(ctx, messageID)
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error fetching message %s: %v\n", messageID, err)
+			os.Exit(1)
+		}
+	}
+
+	if startMsg == nil {
+		fmt.Fprintf(os.Stderr, "Message %s not found\n", messageID)
+		os.Exit(1)
+	}
+
+	// Find the root of the thread by following replies_to chain upward
+	rootMsg := startMsg
+	seen := make(map[string]bool)
+	seen[rootMsg.ID] = true
+
+	for rootMsg.RepliesTo != "" {
+		if seen[rootMsg.RepliesTo] {
+			break // Avoid infinite loops
+		}
+		seen[rootMsg.RepliesTo] = true
+
+		var parentMsg *types.Issue
+		if daemonClient != nil {
+			resp, err := daemonClient.Show(&rpc.ShowArgs{ID: rootMsg.RepliesTo})
+			if err != nil {
+				break // Parent not found, use current as root
+			}
+			if err := json.Unmarshal(resp.Data, &parentMsg); err != nil {
+				break
+			}
+		} else {
+			parentMsg, _ = store.GetIssue(ctx, rootMsg.RepliesTo)
+		}
+		if parentMsg == nil {
+			break
+		}
+		rootMsg = parentMsg
+	}
+
+	// Now collect all messages in the thread
+	// Start from root and find all replies
+	threadMessages := []*types.Issue{rootMsg}
+	threadIDs := map[string]bool{rootMsg.ID: true}
+	queue := []string{rootMsg.ID}
+
+	// BFS to find all replies
+	for len(queue) > 0 {
+		currentID := queue[0]
+		queue = queue[1:]
+
+		// Find all messages that reply to currentID
+		var replies []*types.Issue
+		if daemonClient != nil {
+			// In daemon mode, search for messages with replies_to = currentID
+			// Use list with a filter (simplified: we'll search all messages)
+			// This is inefficient but works for now
+			listArgs := &rpc.ListArgs{IssueType: "message"}
+			resp, err := daemonClient.List(listArgs)
+			if err == nil {
+				var allMessages []*types.Issue
+				if err := json.Unmarshal(resp.Data, &allMessages); err == nil {
+					for _, msg := range allMessages {
+						if msg.RepliesTo == currentID && !threadIDs[msg.ID] {
+							replies = append(replies, msg)
+						}
+					}
+				}
+			}
+		} else {
+			// Direct mode - search for replies
+			messageType := types.TypeMessage
+			filter := types.IssueFilter{IssueType: &messageType}
+			allMessages, _ := store.SearchIssues(ctx, "", filter)
+			for _, msg := range allMessages {
+				if msg.RepliesTo == currentID && !threadIDs[msg.ID] {
+					replies = append(replies, msg)
+				}
+			}
+		}
+
+		for _, reply := range replies {
+			threadMessages = append(threadMessages, reply)
+			threadIDs[reply.ID] = true
+			queue = append(queue, reply.ID)
+		}
+	}
+
+	// Sort by creation time
+	sort.Slice(threadMessages, func(i, j int) bool {
+		return threadMessages[i].CreatedAt.Before(threadMessages[j].CreatedAt)
+	})
+
+	if jsonOutput {
+		encoder := json.NewEncoder(os.Stdout)
+		encoder.SetIndent("", "  ")
+		_ = encoder.Encode(threadMessages)
+		return
+	}
+
+	// Display the thread
+	cyan := color.New(color.FgCyan).SprintFunc()
+	dim := color.New(color.Faint).SprintFunc()
+
+	fmt.Printf("\n%s Thread: %s\n", cyan("📬"), rootMsg.Title)
+	fmt.Println(strings.Repeat("─", 66))
+
+	for _, msg := range threadMessages {
+		// Show indent based on depth (count replies_to chain)
+		depth := 0
+		parent := msg.RepliesTo
+		for parent != "" && depth < 5 {
+			depth++
+			// Find parent to get its replies_to
+			for _, m := range threadMessages {
+				if m.ID == parent {
+					parent = m.RepliesTo
+					break
+				}
+			}
+		}
+		indent := strings.Repeat("  ", depth)
+
+		// Format timestamp
+		timeStr := msg.CreatedAt.Format("2006-01-02 15:04")
+
+		// Status indicator
+		statusIcon := "📧"
+		if msg.Status == types.StatusClosed {
+			statusIcon = "✓"
+		}
+
+		fmt.Printf("%s%s %s %s\n", indent, statusIcon, cyan(msg.ID), dim(timeStr))
+		fmt.Printf("%s  From: %s  To: %s\n", indent, msg.Sender, msg.Assignee)
+		if msg.RepliesTo != "" {
+			fmt.Printf("%s  Re: %s\n", indent, msg.RepliesTo)
+		}
+		fmt.Printf("%s  %s: %s\n", indent, dim("Subject"), msg.Title)
+		if msg.Description != "" {
+			// Indent the body
+			bodyLines := strings.Split(msg.Description, "\n")
+			for _, line := range bodyLines {
+				fmt.Printf("%s  %s\n", indent, line)
+			}
+		}
+		fmt.Println()
+	}
+
+	fmt.Printf("Total: %d messages in thread\n\n", len(threadMessages))
+}
+
 func init() {
 	showCmd.Flags().Bool("json", false, "Output JSON format")
+	showCmd.Flags().Bool("thread", false, "Show full conversation thread (for messages)")
 	rootCmd.AddCommand(showCmd)
 
 	updateCmd.Flags().StringP("status", "s", "", "New status")

internal/hooks/hooks.go

@@ -0,0 +1,161 @@
+// Package hooks provides a hook system for extensibility.
+// Hooks are executable scripts in .beads/hooks/ that run after certain events.
+package hooks
+
+import (
+	"bytes"
+	"context"
+	"encoding/json"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"time"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// Event types
+const (
+	EventCreate  = "create"
+	EventUpdate  = "update"
+	EventClose   = "close"
+	EventMessage = "message"
+)
+
+// Hook file names
+const (
+	HookOnCreate  = "on_create"
+	HookOnUpdate  = "on_update"
+	HookOnClose   = "on_close"
+	HookOnMessage = "on_message"
+)
+
+// Runner handles hook execution
+type Runner struct {
+	hooksDir string
+	timeout  time.Duration
+}
+
+// NewRunner creates a new hook runner.
+// hooksDir is typically .beads/hooks/ relative to workspace root.
+func NewRunner(hooksDir string) *Runner {
+	return &Runner{
+		hooksDir: hooksDir,
+		timeout:  10 * time.Second,
+	}
+}
+
+// NewRunnerFromWorkspace creates a hook runner for a workspace.
+func NewRunnerFromWorkspace(workspaceRoot string) *Runner {
+	return NewRunner(filepath.Join(workspaceRoot, ".beads", "hooks"))
+}
+
+// Run executes a hook if it exists.
+// Runs asynchronously - returns immediately, hook runs in background.
+func (r *Runner) Run(event string, issue *types.Issue) {
+	hookName := eventToHook(event)
+	if hookName == "" {
+		return
+	}
+
+	hookPath := filepath.Join(r.hooksDir, hookName)
+
+	// Check if hook exists and is executable
+	info, err := os.Stat(hookPath)
+	if err != nil || info.IsDir() {
+		return // Hook doesn't exist, skip silently
+	}
+
+	// Check if executable (Unix)
+	if info.Mode()&0111 == 0 {
+		return // Not executable, skip
+	}
+
+	// Run asynchronously
+	go r.runHook(hookPath, event, issue)
+}
+
+// RunSync executes a hook synchronously and returns any error.
+// Useful for testing or when you need to wait for the hook.
+func (r *Runner) RunSync(event string, issue *types.Issue) error {
+	hookName := eventToHook(event)
+	if hookName == "" {
+		return nil
+	}
+
+	hookPath := filepath.Join(r.hooksDir, hookName)
+
+	// Check if hook exists and is executable
+	info, err := os.Stat(hookPath)
+	if err != nil || info.IsDir() {
+		return nil // Hook doesn't exist, skip silently
+	}
+
+	if info.Mode()&0111 == 0 {
+		return nil // Not executable, skip
+	}
+
+	return r.runHook(hookPath, event, issue)
+}
+
+func (r *Runner) runHook(hookPath, event string, issue *types.Issue) error {
+	ctx, cancel := context.WithTimeout(context.Background(), r.timeout)
+	defer cancel()
+
+	// Prepare JSON data for stdin
+	issueJSON, err := json.Marshal(issue)
+	if err != nil {
+		return err
+	}
+
+	// Create command: hook_script <issue_id> <event_type>
+	// #nosec G204 -- hookPath is from controlled .beads/hooks directory
+	cmd := exec.CommandContext(ctx, hookPath, issue.ID, event)
+	cmd.Stdin = bytes.NewReader(issueJSON)
+
+	// Capture output for debugging (but don't block on it)
+	var stdout, stderr bytes.Buffer
+	cmd.Stdout = &stdout
+	cmd.Stderr = &stderr
+
+	// Run the hook
+	err = cmd.Run()
+	if err != nil {
+		// Log error but don't fail - hooks shouldn't break beads
+		// In production, this could go to a log file
+		return err
+	}
+
+	return nil
+}
+
+// HookExists checks if a hook exists for an event
+func (r *Runner) HookExists(event string) bool {
+	hookName := eventToHook(event)
+	if hookName == "" {
+		return false
+	}
+
+	hookPath := filepath.Join(r.hooksDir, hookName)
+	info, err := os.Stat(hookPath)
+	if err != nil || info.IsDir() {
+		return false
+	}
+
+	return info.Mode()&0111 != 0
+}
+
+func eventToHook(event string) string {
+	switch event {
+	case EventCreate:
+		return HookOnCreate
+	case EventUpdate:
+		return HookOnUpdate
+	case EventClose:
+		return HookOnClose
+	case EventMessage:
+		return HookOnMessage
+	default:
+		return ""
+	}
+}

internal/rpc/protocol.go

@@ -72,6 +72,10 @@ type CreateArgs struct {
 	EstimatedMinutes   *int     `json:"estimated_minutes,omitempty"` // Time estimate in minutes
 	Labels             []string `json:"labels,omitempty"`
 	Dependencies       []string `json:"dependencies,omitempty"`
+	// Messaging fields (bd-kwro)
+	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
 }
 
 // UpdateArgs represents arguments for the update operation
@@ -91,6 +95,10 @@ type UpdateArgs struct {
 	AddLabels          []string `json:"add_labels,omitempty"`
 	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)
+	Ephemeral *bool   `json:"ephemeral,omitempty"`  // Can be bulk-deleted when closed
+	RepliesTo *string `json:"replies_to,omitempty"` // Issue ID for conversation threading
 }
 
 // CloseArgs represents arguments for the close operation

internal/rpc/server_issues_epics.go

@@ -76,6 +76,16 @@ func updatesFromArgs(a UpdateArgs) map[string]interface{} {
 	if a.IssueType != nil {
 		u["issue_type"] = *a.IssueType
 	}
+	// Messaging fields (bd-kwro)
+	if a.Sender != nil {
+		u["sender"] = *a.Sender
+	}
+	if a.Ephemeral != nil {
+		u["ephemeral"] = *a.Ephemeral
+	}
+	if a.RepliesTo != nil {
+		u["replies_to"] = *a.RepliesTo
+	}
 	return u
 }
 
@@ -150,6 +160,10 @@ func (s *Server) handleCreate(req *Request) Response {
 		ExternalRef:        externalRef,
 		EstimatedMinutes:   createArgs.EstimatedMinutes,
 		Status:             types.StatusOpen,
+		// Messaging fields (bd-kwro)
+		Sender:    createArgs.Sender,
+		Ephemeral: createArgs.Ephemeral,
+		RepliesTo: createArgs.RepliesTo,
 	}
 	
 	// Check if any dependencies are discovered-from type