Add two-clone collision test proving beads multi-agent workflow failure

- Creates TestTwoCloneCollision integration test
- Sets up 2 independent clones with git hooks and daemons
- Both file issues with same ID (test-1)
- Demonstrates databases don't converge after collision resolution
- Clone A: test-1='Issue from clone A', test-2='Issue from clone B'
- Clone B: test-1='Issue from clone B', test-2='Issue from clone A'
- Git status shows dirty state in both clones
- Test proves beads fails at basic multi-agent workflow

Also adds --json flag to create, ready, and list commands for
better test integration.

Amp-Thread-ID: https://ampcode.com/threads/T-8fa0ab6c-2226-4f9b-8e11-14e1156537fc
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/create.go

@@ -63,6 +63,7 @@ var createCmd = &cobra.Command{
 		externalRef, _ := cmd.Flags().GetString("external-ref")
 		deps, _ := cmd.Flags().GetStringSlice("deps")
 		forceCreate, _ := cmd.Flags().GetBool("force")
+		jsonOutput, _ := cmd.Flags().GetBool("json")
 
 		// Validate explicit ID format if provided (prefix-number)
 		if explicitID != "" {
@@ -245,5 +246,6 @@ func init() {
 	createCmd.Flags().String("external-ref", "", "External reference (e.g., 'gh-9', 'jira-ABC')")
 	createCmd.Flags().StringSlice("deps", []string{}, "Dependencies in format 'type:id' or 'id' (e.g., 'discovered-from:bd-20,blocks:bd-15' or 'bd-20')")
 	createCmd.Flags().Bool("force", false, "Force creation even if prefix doesn't match database prefix")
+	createCmd.Flags().Bool("json", false, "Output JSON format")
 	rootCmd.AddCommand(createCmd)
 }

cmd/bd/list.go

@@ -46,6 +46,7 @@ var listCmd = &cobra.Command{
 		labelsAny, _ := cmd.Flags().GetStringSlice("label-any")
 		titleSearch, _ := cmd.Flags().GetString("title")
 	idFilter, _ := cmd.Flags().GetString("id")
+		jsonOutput, _ := cmd.Flags().GetBool("json")
 
 		// Normalize labels: trim, dedupe, remove empty
 		labels = normalizeLabels(labels)
@@ -211,6 +212,7 @@ func init() {
 	listCmd.Flags().IntP("limit", "n", 0, "Limit results")
 	listCmd.Flags().String("format", "", "Output format: 'digraph' (for golang.org/x/tools/cmd/digraph), 'dot' (Graphviz), or Go template")
 	listCmd.Flags().Bool("all", false, "Show all issues (default behavior; flag provided for CLI familiarity)")
+	listCmd.Flags().Bool("json", false, "Output JSON format")
 	rootCmd.AddCommand(listCmd)
 }
 

cmd/bd/ready.go

@@ -20,6 +20,7 @@ var readyCmd = &cobra.Command{
 		limit, _ := cmd.Flags().GetInt("limit")
 		assignee, _ := cmd.Flags().GetString("assignee")
 		sortPolicy, _ := cmd.Flags().GetString("sort")
+		jsonOutput, _ := cmd.Flags().GetBool("json")
 
 		filter := types.WorkFilter{
 			// Leave Status empty to get both 'open' and 'in_progress' (bd-165)
@@ -293,6 +294,7 @@ func init() {
 	readyCmd.Flags().IntP("priority", "p", 0, "Filter by priority")
 	readyCmd.Flags().StringP("assignee", "a", "", "Filter by assignee")
 	readyCmd.Flags().StringP("sort", "s", "hybrid", "Sort policy: hybrid (default), priority, oldest")
+	readyCmd.Flags().Bool("json", false, "Output JSON format")
 
 	rootCmd.AddCommand(readyCmd)
 	rootCmd.AddCommand(blockedCmd)