Fix: Change default JSONL filename from beads.jsonl to issues.jsonl

The canonical beads database name is issues.jsonl. Tens of thousands of users
have issues.jsonl, and beads.jsonl was only used by the Beads project itself
due to git history pollution.

Changes:
- Updated bd doctor to warn about beads.jsonl instead of issues.jsonl
- Changed default config from beads.jsonl to issues.jsonl
- Reversed precedence in checkGitForIssues to prefer issues.jsonl
- Updated git merge driver config to use issues.jsonl
- Updated all tests to expect issues.jsonl as the default

issues.jsonl is now the canonical default; beads.jsonl is legacy

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

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

cmd/bd/deletion_tracking_test.go

@@ -19,8 +19,8 @@ func TestMultiWorkspaceDeletionSync(t *testing.T) {
 	cloneADir := t.TempDir()
 	cloneBDir := t.TempDir()
 
-	cloneAJSONL := filepath.Join(cloneADir, "beads.jsonl")
-	cloneBJSONL := filepath.Join(cloneBDir, "beads.jsonl")
+	cloneAJSONL := filepath.Join(cloneADir, "issues.jsonl")
+	cloneBJSONL := filepath.Join(cloneBDir, "issues.jsonl")
 
 	cloneADB := filepath.Join(cloneADir, "beads.db")
 	cloneBDB := filepath.Join(cloneBDir, "beads.db")
@@ -177,7 +177,7 @@ func TestMultiWorkspaceDeletionSync(t *testing.T) {
 // Remote deletes an issue, but local has modified it
 func TestDeletionWithLocalModification(t *testing.T) {
 	dir := t.TempDir()
-	jsonlPath := filepath.Join(dir, "beads.jsonl")
+	jsonlPath := filepath.Join(dir, "issues.jsonl")
 	dbPath := filepath.Join(dir, "beads.db")
 
 	ctx := context.Background()
@@ -343,7 +343,7 @@ func TestComputeAcceptedDeletions_LocallyModified(t *testing.T) {
 // TestSnapshotManagement tests the snapshot file lifecycle
 func TestSnapshotManagement(t *testing.T) {
 	dir := t.TempDir()
-	jsonlPath := filepath.Join(dir, "beads.jsonl")
+	jsonlPath := filepath.Join(dir, "issues.jsonl")
 
 	// Write initial JSONL
 	content := `{"id":"bd-1","title":"Test"}