Fix widespread double JSON encoding bug in daemon RPC calls (bd-1048, bd-4ec8)

Multiple CLI commands had a systematic bug where ResolveID responses were
incorrectly converted using string(resp.Data) instead of json.Unmarshal.
Since resp.Data is json.RawMessage (already JSON-encoded), this preserved
the JSON quotes, causing IDs to become "bd-1048" instead of bd-1048.
When re-marshaled for subsequent RPC calls, these became double-quoted
("\"bd-1048\""), causing database lookups to fail.

Bugs fixed:
1. Nil pointer dereference in handleShow - added nil check after GetIssue
2. Double JSON encoding in 12 locations across 4 commands:
   - bd show (3 instances in show.go)
   - bd dep add/remove/tree (5 instances in dep.go)
   - bd label add/remove/list (3 instances in label.go)
   - bd reopen (1 instance in reopen.go)

All instances replaced string(resp.Data) with proper json.Unmarshal.
Removed debug logging added during investigation.

Tested: All affected commands now work correctly with daemon mode.

cmd/bd/dep.go

@@ -3,6 +3,7 @@ package main
 
 import (
 	"context"
+	"encoding/json"
 	"fmt"
 	"os"
 	"strings"
@@ -38,7 +39,10 @@ var depAddCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving issue ID %s: %v\n", args[0], err)
 				os.Exit(1)
 			}
-			fromID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &fromID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 			
 			resolveArgs = &rpc.ResolveIDArgs{ID: args[1]}
 			resp, err = daemonClient.ResolveID(resolveArgs)
@@ -46,7 +50,10 @@ var depAddCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving dependency ID %s: %v\n", args[1], err)
 				os.Exit(1)
 			}
-			toID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &toID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 		} else {
 			var err error
 			fromID, err = utils.ResolvePartialID(ctx, store, args[0])
@@ -159,7 +166,10 @@ var depRemoveCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving issue ID %s: %v\n", args[0], err)
 				os.Exit(1)
 			}
-			fromID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &fromID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 			
 			resolveArgs = &rpc.ResolveIDArgs{ID: args[1]}
 			resp, err = daemonClient.ResolveID(resolveArgs)
@@ -167,7 +177,10 @@ var depRemoveCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving dependency ID %s: %v\n", args[1], err)
 				os.Exit(1)
 			}
-			toID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &toID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 		} else {
 			var err error
 			fromID, err = utils.ResolvePartialID(ctx, store, args[0])
@@ -250,7 +263,10 @@ var depTreeCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving issue ID %s: %v\n", args[0], err)
 				os.Exit(1)
 			}
-			fullID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &fullID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 		} else {
 			var err error
 			fullID, err = utils.ResolvePartialID(ctx, store, args[0])

cmd/bd/label.go

@@ -83,7 +83,10 @@ var labelAddCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving %s: %v\n", id, err)
 					continue
 				}
-				fullID = string(resp.Data)
+				if err := json.Unmarshal(resp.Data, &fullID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					continue
+				}
 			} else {
 				fullID, err = utils.ResolvePartialID(ctx, store, id)
 				if err != nil {
@@ -125,7 +128,10 @@ var labelRemoveCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving %s: %v\n", id, err)
 					continue
 				}
-				fullID = string(resp.Data)
+				if err := json.Unmarshal(resp.Data, &fullID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					continue
+				}
 			} else {
 				fullID, err = utils.ResolvePartialID(ctx, store, id)
 				if err != nil {
@@ -162,7 +168,10 @@ var labelListCmd = &cobra.Command{
 				fmt.Fprintf(os.Stderr, "Error resolving issue ID %s: %v\n", args[0], err)
 				os.Exit(1)
 			}
-			issueID = string(resp.Data)
+			if err := json.Unmarshal(resp.Data, &issueID); err != nil {
+				fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+				os.Exit(1)
+			}
 		} else {
 			var err error
 			issueID, err = utils.ResolvePartialID(ctx, store, args[0])

cmd/bd/reopen.go

@@ -30,7 +30,12 @@ This is more explicit than 'bd update --status open' and emits a Reopened event.
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			var err error

cmd/bd/show.go

@@ -31,7 +31,12 @@ var showCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			// In direct mode, resolve via storage
@@ -369,7 +374,12 @@ var updateCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			var err error
@@ -650,7 +660,12 @@ var closeCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			var err error

internal/rpc/server_export_import_auto.go

@@ -191,10 +191,8 @@ func (s *Server) checkAndAutoImportIfStale(req *Request) error {
 	// If import is already running, skip and let the request proceed (bd-8931)
 	// This prevents blocking RPC requests when import is in progress
 	if !s.importInProgress.CompareAndSwap(false, true) {
-		fmt.Fprintf(os.Stderr, "Debug: auto-import already in progress, skipping (bd-1048)\n")
 		return nil
 	}
-	fmt.Fprintf(os.Stderr, "Debug: acquired import lock, proceeding with auto-import (bd-1048)\n")
 
 	// Track whether we should release the lock via defer
 	// Set to false if we manually release early to avoid double-release bug
@@ -215,23 +213,16 @@ func (s *Server) checkAndAutoImportIfStale(req *Request) error {
 		s.importInProgress.Store(false)
 		shouldDeferRelease = false
 
-		if os.Getenv("BD_DEBUG") != "" {
-			fmt.Fprintf(os.Stderr, "Debug: skipping auto-import, .beads files have uncommitted changes\n")
-		}
 		fmt.Fprintf(os.Stderr, "Warning: auto-import skipped - .beads files have uncommitted changes. Run 'bd import' manually after committing.\n")
 		return nil
 	}
 
 	// Double-check staleness after acquiring lock (another goroutine may have imported)
-	fmt.Fprintf(os.Stderr, "Debug: checking staleness after lock acquisition (bd-1048)\n")
 	isStale, err = autoimport.CheckStaleness(ctx, store, dbPath)
 	if err != nil || !isStale {
-		fmt.Fprintf(os.Stderr, "Debug: staleness check returned: stale=%v err=%v (bd-1048)\n", isStale, err)
 		return err
 	}
 
-	fmt.Fprintf(os.Stderr, "Debug: daemon detected stale JSONL, auto-importing with timeout... (bd-1048)\n")
-
 	// Create timeout context for import operation (bd-8931, bd-1048)
 	// This prevents daemon from hanging if import gets stuck
 	// Use shorter timeout (5s) to ensure client doesn't timeout waiting for response

internal/rpc/server_issues_epics.go

@@ -385,6 +385,12 @@ func (s *Server) handleShow(req *Request) Response {
 			Error:   fmt.Sprintf("failed to get issue: %v", err),
 		}
 	}
+	if issue == nil {
+		return Response{
+			Success: false,
+			Error:   fmt.Sprintf("issue not found: %s", showArgs.ID),
+		}
+	}
 
 	// Populate labels, dependencies, and dependents
 	labels, _ := store.GetLabels(ctx, issue.ID)

internal/rpc/server_lifecycle_conn.go

@@ -178,9 +178,7 @@ func (s *Server) handleSignals() {
 }
 
 func (s *Server) handleConnection(conn net.Conn) {
-	fmt.Fprintf(os.Stderr, "Debug: handleConnection started (bd-1048)\n")
 	defer func() { 
-		fmt.Fprintf(os.Stderr, "Debug: handleConnection closing (bd-1048)\n")
 		_ = conn.Close() 
 	}()
 
@@ -196,19 +194,15 @@ func (s *Server) handleConnection(conn net.Conn) {
 	writer := bufio.NewWriter(conn)
 
 	for {
-		fmt.Fprintf(os.Stderr, "Debug: waiting for request (bd-1048)\n")
 		// Set read deadline for the next request
 		if err := conn.SetReadDeadline(time.Now().Add(s.requestTimeout)); err != nil {
-			fmt.Fprintf(os.Stderr, "Debug: SetReadDeadline error: %v (bd-1048)\n", err)
 			return
 		}
 
 		line, err := reader.ReadBytes('\n')
 		if err != nil {
-			fmt.Fprintf(os.Stderr, "Debug: ReadBytes error: %v (bd-1048)\n", err)
 			return
 		}
-		fmt.Fprintf(os.Stderr, "Debug: received request line (bd-1048)\n")
 
 		var req Request
 		if err := json.Unmarshal(line, &req); err != nil {
@@ -219,18 +213,14 @@ func (s *Server) handleConnection(conn net.Conn) {
 			s.writeResponse(writer, resp)
 			continue
 		}
-		fmt.Fprintf(os.Stderr, "Debug: parsed request operation: %s (bd-1048)\n", req.Operation)
 
 		// Set write deadline for the response
 		if err := conn.SetWriteDeadline(time.Now().Add(s.requestTimeout)); err != nil {
-			fmt.Fprintf(os.Stderr, "Debug: SetWriteDeadline error: %v (bd-1048)\n", err)
 			return
 		}
 
 		resp := s.handleRequest(&req)
-		fmt.Fprintf(os.Stderr, "Debug: handleRequest returned, writing response (bd-1048)\n")
 		s.writeResponse(writer, resp)
-		fmt.Fprintf(os.Stderr, "Debug: response written (bd-1048)\n")
 	}
 }
 

internal/rpc/server_routing_validation_diagnostics.go

@@ -103,8 +103,6 @@ func (s *Server) validateDatabaseBinding(req *Request) error {
 }
 
 func (s *Server) handleRequest(req *Request) Response {
-	fmt.Fprintf(os.Stderr, "Debug: handleRequest called for operation: %s (bd-1048)\n", req.Operation)
-	
 	// Track request timing
 	start := time.Now()
 
@@ -112,7 +110,6 @@ func (s *Server) handleRequest(req *Request) Response {
 	defer func() {
 		latency := time.Since(start)
 		s.metrics.RecordRequest(req.Operation, latency)
-		fmt.Fprintf(os.Stderr, "Debug: handleRequest completed for operation: %s in %v (bd-1048)\n", req.Operation, latency)
 	}()
 
 	// Validate database binding (skip for health/metrics to allow diagnostics)