fix(multi-repo): filter issues by prefix when flushing from non-primary repos (GH #437)

In multi-repo mode, non-primary repos incorrectly wrote ALL issues to their
local issues.jsonl, including foreign issues from other repos. This caused
prefix mismatch errors on subsequent imports.

The fix adds prefix filtering in flushToJSONLWithState() when:
1. Multi-repo mode is configured (repos.primary set)
2. Current repo is not the primary repo
3. The repo has a configured issue_prefix

Issues not matching the local prefix are filtered out before writing to JSONL.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/deletion_tracking_test.go

@@ -834,3 +834,159 @@ func TestMultiRepoSnapshotIsolation(t *testing.T) {
 		t.Error("Repo2 left snapshot has wrong issues")
 	}
 }
+
+// TestMultiRepoFlushPrefixFiltering tests that non-primary repos only flush issues
+// with their own prefix (GH #437 fix).
+//
+// The bug: In multi-repo mode, when a non-primary repo flushes, it incorrectly writes
+// ALL issues (including from primary) to its local issues.jsonl. This causes prefix
+// mismatch errors on subsequent imports.
+//
+// Expected behavior:
+// - Primary repo: writes all issues (from all repos)
+// - Non-primary repos: only writes issues matching their prefix
+func TestMultiRepoFlushPrefixFiltering(t *testing.T) {
+	// Setup workspace directories
+	primaryDir := t.TempDir()
+	additionalDir := t.TempDir()
+
+	// Setup .beads directories
+	primaryBeadsDir := filepath.Join(primaryDir, ".beads")
+	additionalBeadsDir := filepath.Join(additionalDir, ".beads")
+	if err := os.MkdirAll(primaryBeadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create primary .beads dir: %v", err)
+	}
+	if err := os.MkdirAll(additionalBeadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create additional .beads dir: %v", err)
+	}
+
+	// Create database in additional (non-primary) dir
+	dbPath := filepath.Join(additionalBeadsDir, "beads.db")
+	ctx := context.Background()
+
+	store, err := sqlite.New(context.Background(), dbPath)
+	if err != nil {
+		t.Fatalf("Failed to create store: %v", err)
+	}
+	defer store.Close()
+
+	// Set prefix for additional repo (different from primary)
+	if err := store.SetConfig(ctx, "issue_prefix", "foo-b"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	// Setup multi-repo config
+	config.Set("repos.primary", primaryDir)
+	config.Set("repos.additional", []string{additionalDir})
+	defer func() {
+		config.Set("repos.primary", "")
+		config.Set("repos.additional", nil)
+	}()
+
+	// Create issues with different prefixes (simulating hydrated multi-repo)
+	// foo-a prefix = primary repo issues (hydrated from remote)
+	// foo-b prefix = additional repo issues (local)
+	primaryIssue := &types.Issue{
+		ID:          "foo-a-001",
+		Title:       "Primary repo issue",
+		Description: "This belongs to primary",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   "task",
+		SourceRepo:  ".",
+	}
+
+	additionalIssue := &types.Issue{
+		ID:          "foo-b-001",
+		Title:       "Additional repo issue",
+		Description: "This belongs to additional",
+		Status:      types.StatusOpen,
+		Priority:    1,
+		IssueType:   "task",
+		SourceRepo:  additionalDir,
+	}
+
+	// Use batch create with SkipPrefixValidation to simulate multi-repo hydration
+	// (in real multi-repo mode, issues from other repos are imported with prefix validation skipped)
+	if err := store.CreateIssuesWithFullOptions(ctx, []*types.Issue{primaryIssue, additionalIssue}, "test", sqlite.BatchCreateOptions{SkipPrefixValidation: true}); err != nil {
+		t.Fatalf("Failed to batch create issues: %v", err)
+	}
+
+	// Build issues slice (simulating what flushToJSONLWithState does)
+	allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		t.Fatalf("Failed to search issues: %v", err)
+	}
+	if len(allIssues) != 2 {
+		t.Fatalf("Expected 2 issues, got %d", len(allIssues))
+	}
+
+	// Get configured prefix for this repo (additional)
+	prefix, err := store.GetConfig(ctx, "issue_prefix")
+	if err != nil {
+		t.Fatalf("Failed to get prefix: %v", err)
+	}
+
+	// Determine if we're primary (we're not - we're in additional)
+	cwd := additionalDir // Simulate being in additional repo
+	primaryPath := config.GetMultiRepoConfig().Primary
+	absCwd, _ := filepath.Abs(cwd)
+	absPrimary, _ := filepath.Abs(primaryPath)
+	isPrimary := absCwd == absPrimary
+
+	if isPrimary {
+		t.Fatal("Expected to be non-primary repo")
+	}
+
+	// Filter issues by prefix (the fix)
+	filtered := make([]*types.Issue, 0, len(allIssues))
+	prefixWithDash := prefix + "-"
+	for _, issue := range allIssues {
+		if len(issue.ID) >= len(prefixWithDash) && issue.ID[:len(prefixWithDash)] == prefixWithDash {
+			filtered = append(filtered, issue)
+		}
+	}
+
+	// Verify filtering worked
+	if len(filtered) != 1 {
+		t.Errorf("Expected 1 filtered issue, got %d", len(filtered))
+	}
+	if len(filtered) > 0 && filtered[0].ID != "foo-b-001" {
+		t.Errorf("Expected filtered issue to be foo-b-001, got %s", filtered[0].ID)
+	}
+
+	// Write filtered issues to additional repo's JSONL
+	jsonlPath := filepath.Join(additionalBeadsDir, "issues.jsonl")
+	f, err := os.Create(jsonlPath)
+	if err != nil {
+		t.Fatalf("Failed to create JSONL: %v", err)
+	}
+	encoder := json.NewEncoder(f)
+	for _, issue := range filtered {
+		if err := encoder.Encode(issue); err != nil {
+			f.Close()
+			t.Fatalf("Failed to encode issue: %v", err)
+		}
+	}
+	f.Close()
+
+	// Read back and verify only foo-b issue is present
+	data, err := os.ReadFile(jsonlPath)
+	if err != nil {
+		t.Fatalf("Failed to read JSONL: %v", err)
+	}
+
+	var readIssue types.Issue
+	if err := json.Unmarshal(data, &readIssue); err != nil {
+		t.Fatalf("Failed to parse JSONL: %v", err)
+	}
+
+	if readIssue.ID != "foo-b-001" {
+		t.Errorf("JSONL contains wrong issue: expected foo-b-001, got %s", readIssue.ID)
+	}
+
+	// Verify foo-a issue is NOT in the file
+	if string(data[:10]) == `{"id":"foo-a` {
+		t.Error("JSONL incorrectly contains foo-a issue (GH #437 bug)")
+	}
+}