feat(builder): add pre-clean step to proto generation to remove stale files

Introduce CleanXatuCBTProtos and CleanCBTAPIGenerated helpers that wipe
generated proto, handler, server and OpenAPI artefacts before each
regeneration. This prevents stale outputs from persisting when schemas
or templates change, reducing hard-to-debug mismatches between source
and generated code.

Author: mattevans

pkg/builder/manager.go

@@ -224,13 +224,32 @@ func (m *Manager) BuildLabFrontend(ctx context.Context) error {
 func (m *Manager) GenerateXatuCBTProtos(ctx context.Context) error {
 	m.log.WithField("repo", "xatu-cbt").Info("generating protos")
 
+	// Clean generated proto files before regenerating to avoid stale files
+	if err := m.CleanXatuCBTProtos(); err != nil {
+		m.log.WithError(err).Warn("failed to clean xatu-cbt protos, continuing anyway")
+	}
+
 	if err := m.runMake(ctx, m.cfg.Repos.XatuCBT, "proto"); err != nil {
 		return fmt.Errorf("failed to generate xatu-cbt protos: %w", err)
 	}
 
 	return nil
 }
 
+// CleanXatuCBTProtos removes generated proto files from xatu-cbt.
+func (m *Manager) CleanXatuCBTProtos() error {
+	m.log.WithField("repo", "xatu-cbt").Info("cleaning generated proto files")
+
+	// xatu-cbt generates protos to pkg/proto/clickhouse/
+	protoDir := filepath.Join(m.cfg.Repos.XatuCBT, "pkg", "proto", "clickhouse")
+
+	if err := os.RemoveAll(protoDir); err != nil {
+		return fmt.Errorf("failed to remove xatu-cbt proto directory: %w", err)
+	}
+
+	return nil
+}
+
 // GenerateProtos generates protobuf files for cbt-api.
 func (m *Manager) GenerateProtos(ctx context.Context) error {
 	// Generate cbt-api protos (only for first network, they're network-agnostic)
@@ -242,6 +261,11 @@ func (m *Manager) GenerateProtos(ctx context.Context) error {
 		"network": network.Name,
 	}).Info("generating protos")
 
+	// Clean generated files before regenerating to avoid stale files
+	if err := m.CleanCBTAPIGenerated(); err != nil {
+		m.log.WithError(err).Warn("failed to clean cbt-api generated files, continuing anyway")
+	}
+
 	// Use the generated config file
 	configPath := filepath.Join(".xcli", "configs", fmt.Sprintf("cbt-api-%s.yaml", network.Name))
 
@@ -262,6 +286,40 @@ func (m *Manager) GenerateProtos(ctx context.Context) error {
 	return nil
 }
 
+// CleanCBTAPIGenerated removes all generated files from cbt-api.
+// This includes proto files, handlers, server implementation, and OpenAPI specs.
+func (m *Manager) CleanCBTAPIGenerated() error {
+	m.log.WithField("repo", "cbt-api").Info("cleaning generated files")
+
+	// Files and directories to remove (matches cbt-api Makefile clean target)
+	toRemove := []string{
+		// Proto generated directory
+		filepath.Join(m.cfg.Repos.CBTAPI, "pkg", "proto", "clickhouse"),
+		// Generated handler code
+		filepath.Join(m.cfg.Repos.CBTAPI, "internal", "handlers", "generated.go"),
+		// Generated server implementation
+		filepath.Join(m.cfg.Repos.CBTAPI, "internal", "server", "implementation.go"),
+		// Embedded OpenAPI spec
+		filepath.Join(m.cfg.Repos.CBTAPI, "internal", "server", "openapi.yaml"),
+		// Root OpenAPI spec
+		filepath.Join(m.cfg.Repos.CBTAPI, "openapi.yaml"),
+		// Proto descriptors
+		filepath.Join(m.cfg.Repos.CBTAPI, ".descriptors.pb"),
+		// Discovered tables cache
+		filepath.Join(m.cfg.Repos.CBTAPI, ".tables.txt"),
+		// Temp directory
+		filepath.Join(m.cfg.Repos.CBTAPI, "tmp"),
+	}
+
+	for _, path := range toRemove {
+		if err := os.RemoveAll(path); err != nil {
+			m.log.WithError(err).WithField("path", path).Warn("failed to remove generated file")
+		}
+	}
+
+	return nil
+}
+
 // binaryExists checks if a binary file exists.
 func (m *Manager) binaryExists(path string) bool {
 	info, err := os.Stat(path)