Fix issue-prefix config fallback to config.yaml (GH#1145) (#1146)

The config.yaml file uses "issue-prefix" (with hyphen) but this setting
was only read during bd init. After initialization, all code read from
the database's "issue_prefix" key, so subsequent changes to config.yaml
were silently ignored.

This fix adds a fallback to config.yaml's "issue-prefix" in the key
locations where the prefix is retrieved from the database:

1. autoflush.go: Auto-import now checks config.yaml before falling back
   to auto-detection from JSONL or directory name

2. autoflush.go: filterByMultiRepoPrefix now checks config.yaml as fallback

3. create.go: Direct mode prefix validation now checks config.yaml as fallback

Priority order is preserved:
1. Database issue_prefix (if set)
2. Config.yaml issue-prefix (new fallback)
3. Auto-detection from JSONL/directory (existing fallback)

Fixes #1145

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/autoflush.go

@@ -253,8 +253,14 @@ func autoImportIfNewer() {
 	if store != nil {
 		prefix, prefixErr := store.GetConfig(ctx, "issue_prefix")
 		if prefixErr != nil || prefix == "" {
-			// Database needs initialization - detect prefix from JSONL or directory
+			// GH#1145: Check config.yaml for issue-prefix before auto-detecting
-			detectedPrefix := detectPrefixFromJSONL(jsonlData)
+			detectedPrefix := config.GetString("issue-prefix")
+
+			// If config.yaml doesn't have it, try to detect from JSONL
+			if detectedPrefix == "" {
+				detectedPrefix = detectPrefixFromJSONL(jsonlData)
+			}
+
 			if detectedPrefix == "" {
 				// Fallback: detect from directory name
 				beadsDir := filepath.Dir(jsonlPath)
@@ -418,8 +424,6 @@ func autoImportIfNewer() {
 	}
 }
 
-
-
 // markDirtyAndScheduleFlush marks the database as dirty and schedules a flush
 // markDirtyAndScheduleFlush marks the database as dirty and schedules a debounced
 // export to JSONL. Uses FlushManager's event-driven architecture.
@@ -562,7 +566,7 @@ func writeJSONLAtomic(jsonlPath string, issues []*types.Issue) ([]string, error)
 
 	for _, issue := range issues {
 		if err := encoder.Encode(issue); err != nil {
-		 return nil, fmt.Errorf("failed to encode issue %s: %w", issue.ID, err)
+			return nil, fmt.Errorf("failed to encode issue %s: %w", issue.ID, err)
 		}
 
 		exportedIDs = append(exportedIDs, issue.ID)
@@ -726,10 +730,13 @@ func filterByMultiRepoPrefix(ctx context.Context, s storage.Storage, issues []*t
 		return issues
 	}
 
-	// Get our configured prefix
+	// Get our configured prefix (GH#1145: fallback to config.yaml)
 	prefix, prefixErr := s.GetConfig(ctx, "issue_prefix")
 	if prefixErr != nil || prefix == "" {
-		return issues
+		prefix = config.GetString("issue-prefix")
+		if prefix == "" {
+			return issues
+		}
 	}
 
 	// Determine if we're the primary repo

cmd/bd/create.go

@@ -432,8 +432,11 @@ var createCmd = &cobra.Command{
 				}
 				// If error, continue without validation (non-fatal)
 			} else {
-				// Direct mode - check config
+				// Direct mode - check config (GH#1145: fallback to config.yaml)
 				dbPrefix, _ = store.GetConfig(ctx, "issue_prefix")
+				if dbPrefix == "" {
+					dbPrefix = config.GetString("issue-prefix")
+				}
 				allowedPrefixes, _ = store.GetConfig(ctx, "allowed_prefixes")
 			}