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- bd supersede --with: mark issues as superseded with auto-close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/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)