fix: verify types.custom persisted before writing sentinel

internal/beads/beads_types.go

@@ -134,16 +134,30 @@ func EnsureCustomTypes(beadsDir string) error {
 	}
 
 	// Configure custom types via bd CLI
+	bdEnv := append(stripEnvPrefixes(os.Environ(), "BEADS_DIR="), "BEADS_DIR="+beadsDir)
 	cmd := exec.Command("bd", "config", "set", "types.custom", typesList)
 	cmd.Dir = beadsDir
 	// Set BEADS_DIR explicitly to ensure bd operates on the correct database.
 	// Strip inherited BEADS_DIR first — getenv() returns the first match (gt-uygpe).
-	cmd.Env = append(stripEnvPrefixes(os.Environ(), "BEADS_DIR="), "BEADS_DIR="+beadsDir)
+	cmd.Env = bdEnv
 	if output, err := cmd.CombinedOutput(); err != nil {
 		return fmt.Errorf("configure custom types in %s: %s: %w",
 			beadsDir, strings.TrimSpace(string(output)), err)
 	}
 
+	// Verify the config was actually persisted in the database (GH#2637).
+	// bd config set can exit 0 but fail to write if it targets the wrong
+	// database (redirect mismatch, stale metadata, server not running).
+	// Without this check, the sentinel file below would cache a lie,
+	// causing all future EnsureCustomTypes calls to skip re-configuration.
+	verifyCmd := exec.Command("bd", "config", "get", "types.custom")
+	verifyCmd.Dir = beadsDir
+	verifyCmd.Env = bdEnv
+	if verifyOutput, err := verifyCmd.Output(); err != nil || !strings.Contains(string(verifyOutput), "agent") {
+		return fmt.Errorf("types.custom not persisted in %s after bd config set (verify returned %q): db may be misconfigured",
+			beadsDir, strings.TrimSpace(string(verifyOutput)))
+	}
+
 	// Write sentinel file with the types list for staleness detection.
 	// On next invocation, if types have changed, the sentinel won't match
 	// and we'll re-configure automatically.

internal/beads/beads_types_test.go

@@ -53,6 +53,9 @@ switch ($cmd) {
     if ($args.Length -ge 3 -and $args[1] -eq 'get' -and $args[2] -eq 'status.custom') {
       Write-Output ''
     }
+    if ($args.Length -ge 3 -and $args[1] -eq 'get' -and $args[2] -eq 'types.custom') {
+      Write-Output 'agent,role,rig,convoy,slot,queue,event,message,molecule,gate,merge-request'
+    }
     exit 0
   }
   'migrate' { exit 0 }
@@ -92,7 +95,14 @@ case "$cmd" in
     printf 'prefix: %s\nissue-prefix: %s-\n' "$prefix" "$prefix" > "$target/config.yaml"
     exit 0
     ;;
-  config|migrate)
+  config)
+    # Return types list for "config get types.custom" verification
+    if echo "$*" | grep -q "get types.custom"; then
+      echo "agent,role,rig,convoy,slot,queue,event,message,molecule,gate,merge-request"
+    fi
+    exit 0
+    ;;
+  migrate)
     exit 0
     ;;
   *)
@@ -347,6 +357,66 @@ func TestEnsureCustomTypes(t *testing.T) {
 	})
 }
 
+func TestEnsureCustomTypes_VerifyPersistence(t *testing.T) {
+	t.Run("sentinel not written when db verify fails", func(t *testing.T) {
+		// Install a mock bd that succeeds on "config set" but returns empty
+		// on "config get types.custom" — simulating a silent write failure.
+		binDir := t.TempDir()
+		logPath := filepath.Join(binDir, "bd.log")
+		script := `#!/bin/sh
+LOG_FILE='` + logPath + `'
+printf '%s\n' "$*" >> "$LOG_FILE"
+cmd=""
+for arg in "$@"; do
+  case "$arg" in --*) ;; *) cmd="$arg"; break ;; esac
+done
+case "$cmd" in
+  init)
+    target="${BEADS_DIR:-$(pwd)/.beads}"
+    mkdir -p "$target/dolt"
+    printf 'prefix: gt\nissue-prefix: gt-\n' > "$target/config.yaml"
+    exit 0
+    ;;
+  config)
+    # "config set" succeeds but "config get types.custom" returns empty
+    if echo "$*" | grep -q "get types.custom"; then
+      echo ""
+    fi
+    exit 0
+    ;;
+  migrate) exit 0 ;;
+  *) exit 0 ;;
+esac
+`
+		if err := os.WriteFile(filepath.Join(binDir, "bd"), []byte(script), 0755); err != nil {
+			t.Fatalf("write mock bd: %v", err)
+		}
+		t.Setenv("PATH", binDir+string(os.PathListSeparator)+os.Getenv("PATH"))
+
+		tmpDir := t.TempDir()
+		beadsDir := filepath.Join(tmpDir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatal(err)
+		}
+
+		ResetEnsuredDirs()
+
+		err := EnsureCustomTypes(beadsDir)
+		if err == nil {
+			t.Fatal("expected error when types.custom verify fails, got nil")
+		}
+		if !strings.Contains(err.Error(), "not persisted") {
+			t.Fatalf("expected 'not persisted' error, got: %v", err)
+		}
+
+		// Sentinel file should NOT have been written
+		sentinelPath := filepath.Join(beadsDir, typesSentinel)
+		if _, err := os.Stat(sentinelPath); !os.IsNotExist(err) {
+			t.Error("sentinel file should not exist when verify fails")
+		}
+	})
+}
+
 func TestEnsureCustomStatuses(t *testing.T) {
 	ResetEnsuredDirs()