diff --git a/tooling/files.sh b/tooling/files.sh
index 4a0ec799..34dee96c 100644
--- a/tooling/files.sh
+++ b/tooling/files.sh
@@ -3,19 +3,18 @@ set -e
 tool=build/clang-x86_64-pc-windows-msvc/Release/r3_gh_tool
 cmake --build build/clang-x86_64-pc-windows-msvc/Release --target r3_gh_tool
 
-scan_dir=tmps/gh_auto
-file_list=files.txt
-rm -f $file_list
-for file in tmps/gh_auto/*.cxx; do
-    echo $file >>$file_list
-done
-for file in tmps/gh_stub/*.cxx; do
-    echo $file >>$file_list
-done
-for file in tmps/gh_fix/*.cxx; do
-    echo $file >>$file_list
+types=(auto ref fix stub)
+for type in "${types[@]}"; do
+    file_list="files_${type}.txt"
+    rm -f "$file_list"
+
+    if [ -d "tmps/gh_${type}" ]; then
+        for file in "tmps/gh_${type}"/*.cxx; do
+            echo "$file" >>"$file_list"
+        done
+        $tool "@$file_list" -v --type=$type --log-file=log-functions.txt
+    fi
 done
 
-$tool @$file_list -v --log-file=log-functions.txt
 $tool tmps/gh_global.h -mglobals -v --log-file=log-globals.txt
 $tool -mduplicates -v --log-file=log-duplicates.txt
diff --git a/tooling/tool.cpp b/tooling/tool.cpp
index aaf06c18..1d2ea81a 100644
--- a/tooling/tool.cpp
+++ b/tooling/tool.cpp
@@ -18,6 +18,38 @@ extern "C" TSLanguage *tree_sitter_cpp();
 // Global address regex pattern
 const std::regex ADDRESS_REGEX(R"(//\s*([0-9a-fA-F]{8}))");
 
+// Add enum for file types
+enum class FileType { Auto, Fix, Stub, Ref };
+
+// Helper function to convert string to FileType
+FileType stringToFileType(const std::string &type_str) {
+  if (type_str == "auto")
+    return FileType::Auto;
+  if (type_str == "fix")
+    return FileType::Fix;
+  if (type_str == "stub")
+    return FileType::Stub;
+  if (type_str == "ref")
+    return FileType::Ref;
+  throw std::invalid_argument("Invalid file type: " + type_str);
+}
+
+// Helper function to convert FileType to string
+std::string fileTypeToString(FileType type) {
+  switch (type) {
+  case FileType::Auto:
+    return "auto";
+  case FileType::Fix:
+    return "fix";
+  case FileType::Stub:
+    return "stub";
+  case FileType::Ref:
+    return "ref";
+  default:
+    throw std::logic_error(fmt::format("Invalid file type: {}", (int)type));
+  }
+}
+
 // Helper function to check if a comment contains an address
 bool hasAddressPattern(const std::string &comment) {
   return std::regex_search(comment, ADDRESS_REGEX);
@@ -47,6 +79,7 @@ struct FunctionInfo {
   std::string address;
   std::string filepath;
   bool is_import;
+  FileType type; // Add type field
 };
 
 struct GlobalInfo {
@@ -81,11 +114,11 @@ public:
                      &delete_imports_stmt,
                      "Failed to prepare delete imports statement");
     prepareStatement("INSERT OR REPLACE INTO Functions (filepath, name, "
-                     "address) VALUES (?, ?, ?)",
+                     "address, type) VALUES (?, ?, ?, ?)",
                      &insert_functions_stmt,
                      "Failed to prepare insert functions statement");
-    prepareStatement("INSERT OR REPLACE INTO Imports (filepath, name, address) "
-                     "VALUES (?, ?, ?)",
+    prepareStatement("INSERT OR REPLACE INTO Imports (filepath, name, address, "
+                     "type) VALUES (?, ?, ?, ?)",
                      &insert_imports_stmt,
                      "Failed to prepare insert imports statement");
     prepareStatement("DELETE FROM Globals WHERE filepath = ?",
@@ -128,6 +161,7 @@ public:
     sqlite3_bind_text(stmt, 1, func.filepath.c_str(), -1, SQLITE_STATIC);
     sqlite3_bind_text(stmt, 2, func.name.c_str(), -1, SQLITE_STATIC);
     sqlite3_bind_text(stmt, 3, func.address.c_str(), -1, SQLITE_STATIC);
+    sqlite3_bind_int(stmt, 4, static_cast<int>(func.type));
     sqlite3_step(stmt);
   }
 
@@ -157,8 +191,8 @@ public:
     }
 
     const char *create_tables = R"(
-            CREATE TABLE IF NOT EXISTS Functions (filepath TEXT, name TEXT, address TEXT, PRIMARY KEY (name, filepath));
-            CREATE TABLE IF NOT EXISTS Imports (filepath TEXT, name TEXT, address TEXT, PRIMARY KEY (name, filepath));
+            CREATE TABLE IF NOT EXISTS Functions (filepath TEXT, name TEXT, address TEXT, type INTEGER DEFAULT 0, PRIMARY KEY (name, filepath));
+            CREATE TABLE IF NOT EXISTS Imports (filepath TEXT, name TEXT, address TEXT, type INTEGER DEFAULT 0, PRIMARY KEY (name, filepath));
             CREATE TABLE IF NOT EXISTS Globals (filepath TEXT, name TEXT, address TEXT);
         )";
 
@@ -390,7 +424,7 @@ bool hasFunctionBody(TSNode node) {
 }
 
 void findFunctions(TSNode node, const char *source_code, uint32_t source_length,
-                   std::vector<FunctionInfo> &functions) {
+                   std::vector<FunctionInfo> &functions, FileType file_type) {
   const char *type = ts_node_type(node);
 
   if (strcmp(type, "function_definition") == 0 ||
@@ -409,7 +443,8 @@ void findFunctions(TSNode node, const char *source_code, uint32_t source_length,
         FunctionInfo func{func_name, address, "",
                           strcmp(type, "function_definition") == 0
                               ? !hasFunctionBody(node)
-                              : true};
+                              : true,
+                          file_type}; // Add file_type parameter
         functions.push_back(func);
       }
       // We'll never nest function declarations
@@ -422,8 +457,8 @@ void findFunctions(TSNode node, const char *source_code, uint32_t source_length,
 
   uint32_t child_count = ts_node_child_count(node);
   for (uint32_t i = 0; i < child_count; i++) {
-    findFunctions(ts_node_child(node, i), source_code, source_length,
-                  functions);
+    findFunctions(ts_node_child(node, i), source_code, source_length, functions,
+                  file_type);
   }
 }
 
@@ -454,7 +489,8 @@ std::vector<std::string> readFileList(const std::string &list_file) {
   return files;
 }
 
-bool processFile(const std::string &filepath, DatabaseManager &db) {
+bool processFile(const std::string &filepath, DatabaseManager &db,
+                 FileType file_type) {
   std::ifstream file(filepath);
   if (!file.is_open()) {
     spdlog::error("Could not open file {}", filepath);
@@ -482,17 +518,18 @@ bool processFile(const std::string &filepath, DatabaseManager &db) {
 
   std::vector<FunctionInfo> functions;
   findFunctions(root_node, file_content.c_str(), file_content.length(),
-                functions);
+                functions, file_type);
 
   for (auto &func : functions) {
     func.filepath = filepath;
     db.insertFunction(func);
-    spdlog::debug("{}: {} @ {} in {}", func.is_import ? "Import" : "Function",
-                  func.name, func.address, filepath);
+    spdlog::debug("{}: {} @ {} in {} (type: {})",
+                  func.is_import ? "Import" : "Function", func.name,
+                  func.address, filepath, fileTypeToString(func.type));
   }
 
-  spdlog::info("Processed {} functions/imports from {}", functions.size(),
-               filepath);
+  spdlog::info("Processed {} functions/imports from {} (type: {})",
+               functions.size(), filepath, fileTypeToString(file_type));
 
   ts_tree_delete(tree);
   ts_parser_delete(parser);
@@ -741,6 +778,7 @@ int main(int argc, char *argv[]) {
   std::string db_path = "gh.db";
   std::string mode = "functions";
   std::string log_file = "";
+  std::string type_str = "auto"; // Add type string variable
   bool verbose = false;
 
   app.add_option("files", input_files,
@@ -755,11 +793,24 @@ int main(int argc, char *argv[]) {
       ->default_val("functions")
       ->check(
           CLI::IsMember({"functions", "globals", "duplicates", "dump-tree"}));
+  app.add_option("-t,--type", type_str,
+                 "File type: 'auto', 'fix', 'stub', or 'ref'")
+      ->default_val("auto")
+      ->check(CLI::IsMember({"auto", "fix", "stub", "ref"}));
   app.add_flag("-v,--verbose", verbose, "Enable verbose logging (debug level)");
   app.add_flag("--log-file", log_file, "Enable logging to file");
 
   CLI11_PARSE(app, argc, argv);
 
+  // Convert string to FileType enum
+  FileType file_type;
+  try {
+    file_type = stringToFileType(type_str);
+  } catch (const std::invalid_argument &e) {
+    spdlog::error("Invalid file type: {}", type_str);
+    return 1;
+  }
+
   // Set log level based on verbose flag
   if (verbose) {
     spdlog::set_level(spdlog::level::debug);
@@ -830,10 +881,10 @@ int main(int argc, char *argv[]) {
       db.beginTransaction();
 
       for (const auto &filepath : files_to_process) {
-        spdlog::info("=== Processing: {} ===", filepath);
+        spdlog::info("=== Processing: {} (type: {}) ===", filepath, type_str);
         bool success = false;
         if (mode == "functions") {
-          success = processFile(filepath, db);
+          success = processFile(filepath, db, file_type);
         } else if (mode == "globals") {
           success = processGlobalsFile(filepath, db);
         }
@@ -860,6 +911,7 @@ int main(int argc, char *argv[]) {
     spdlog::info("=== Summary ===");
     spdlog::info("Processed {} files successfully", processed_count);
     spdlog::info("Mode: {}", mode);
+    spdlog::info("File type: {}", type_str);
     if (mode != "dump-tree") {
       spdlog::info("Database saved to: {}", db_path);
     }