diff --git a/Makefile b/Makefile
index e10cc45..23af4f0 100644
--- a/Makefile
+++ b/Makefile
@@ -18,21 +18,11 @@ REPLACE_CMD = $(BASHCMD) $(BASH_SCRIPT_DIR)/replace.sh
 CLANG_TIDY_CMD = $(BASHCMD) $(BASH_SCRIPT_DIR)/clang-tidy.sh
 CLANG_FORMAT_CMD = $(BASHCMD) $(BASH_SCRIPT_DIR)/clang-format.sh
 
-
 CLANG_TIDY_CONFIG = $(SRC_DIR)/linter/.clang-tidy
 CLANG_FORMAT_STYLE = $(SRC_DIR)/linter/.clang-format
 
-# COMPILE_COMMANDS_FILE = compile_commands.json
-# ifeq ($(wildcard $(DEBUG_DIR)/$(COMPILE_COMMANDS_FILE)),)
-# 	ifeq ($(wildcard $(RELEASE_DIR)/$(COMPILE_COMMANDS_FILE)),)
-# 		$(info Neither $(DEBUG_DIR)/$(COMPILE_COMMANDS_FILE) nor $(RELEASE_DIR)/$(COMPILE_COMMANDS_FILE) exist. \
-# 		Run make debug or make release first.)
-# 	else
-# 		COMPILE_COMMANDS := $(RELEASE_DIR)/$(COMPILE_COMMANDS_FILE)  
-# 	endif
-# else
-# 	COMPILE_COMMANDS := $(DEBUG_DIR)/$(COMPILE_COMMANDS_FILE)
-# endif
+INCLUDE_LIBS_EXT = "/usr/include/eigen3 /usr/include/catch2 /usr/include/hdf5/serial"
+
 
 all: debug release documentation
 
@@ -64,7 +54,7 @@ documentation:
 linter: clang-tidy clang-format
 
 clang-tidy:
-	$(CLANG_TIDY_CMD) $(PROJECT_DIR) $(COMPILE_COMMANDS) $(CLANG_TIDY_CONFIG) $(SRC_DIR) $(CPP_STD)
+	$(CLANG_TIDY_CMD) $(BUIL_DIR) $(SRC_DIR) $(CLANG_TIDY_CONFIG) $(CPP_STD) $(INCLUDE_LIBS_EXT)
 
 clang-format:
 	$(CLANG_FORMAT_CMD) $(CLANG_FORMAT_STYLE) $(SRC_DIR)
diff --git a/dev/CMakeLists.txt b/dev/CMakeLists.txt
index dbd83d3..0bff515 100644
--- a/dev/CMakeLists.txt
+++ b/dev/CMakeLists.txt
@@ -34,7 +34,9 @@ add_subdirectory(app)
 # Include tests
 add_subdirectory(tests)
 
-
 # Set compile options for different build types
 set(CMAKE_CXX_FLAGS_DEBUG "-g3 -O0 -tr")
-set(CMAKE_CXX_FLAGS_RELEASE "-O3")
\ No newline at end of file
+set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+
+# Write include dirs to a file
+include(cmake/WriteIncludeDirs.cmake)
\ No newline at end of file
diff --git a/dev/app/src/main.cpp b/dev/app/src/main.cpp
index ace9f84..f618a82 100644
--- a/dev/app/src/main.cpp
+++ b/dev/app/src/main.cpp
@@ -1,23 +1,21 @@
+#include <constants/constants.h>
+#include <data_processing/config.h>
+#include <yaml-cpp/yaml.h>
+
+#include <boost/program_options.hpp>
 #include <iostream>
 #include <string>
 #include <tuple>
 #include <vector>
 
-#include <boost/program_options.hpp>
-#include <yaml-cpp/yaml.h>
-
-#include <constants/constants.h>
-#include <data_processing/config.h>
-
 namespace po = boost::program_options;
 namespace dpc = flash::data_processing::config;
 namespace tp = flash::types;
 
 po::variables_map loadCommandLineArguments(int argc, char* argv[]) {
     po::options_description desc("Allowed options");
-    desc.add_options()
-        ("help,h", "produce help message")
-        ("config-file,i", po::value<std::string>()->default_value("config.yaml"), "set path to a config.yaml");
+    desc.add_options()("help,h", "produce help message")(
+        "config-file,i", po::value<std::string>()->default_value("config.yaml"), "set path to a config.yaml");
 
     po::variables_map vm;
     po::store(po::parse_command_line(argc, argv, desc), vm);
@@ -30,33 +28,30 @@ po::variables_map loadCommandLineArguments(int argc, char* argv[]) {
     return vm;
 }
 
-dpc::Config setupConfigParameters(po::variables_map commandLineArguments){
-
+dpc::Config setupConfigParameters(po::variables_map commandLineArguments) {
     auto configFile = commandLineArguments["config-file"].as<std::string>();
     std::cout << "Load configuration from " << configFile << std::endl;
-    try{
-
+    try {
         auto configNode = YAML::LoadFile(configFile);
         auto params = dpc::Config(configNode);
         params.validate();
         return params;
-        
-    } catch (YAML::BadFile BF){
-        std::cerr << "Flash is terminating: " << "Could not open " << configFile << std::endl;
-    } catch (dpc::InvalidKeyException IKE){
+
+    } catch (YAML::BadFile BF) {
+        std::cerr << "Flash is terminating: "
+                  << "Could not open " << configFile << std::endl;
+    } catch (dpc::InvalidKeyException IKE) {
         std::cerr << "Flash is terminating: " << IKE.what() << std::endl;
-    } catch (dpc::MissingKeyException MKE){
+    } catch (dpc::MissingKeyException MKE) {
         std::cerr << "Flash is terminating: " << MKE.what() << std::endl;
-    } catch (dpc::InvalidConfigurationException ICE){
+    } catch (dpc::InvalidConfigurationException ICE) {
         std::cerr << "Flash is terminating: " << ICE.what() << std::endl;
     }
-
 }
 
 int main(int argc, char* argv[]) {
-
     auto commandLineArguments = loadCommandLineArguments(argc, argv);
-    auto configParameters     = setupConfigParameters(commandLineArguments);
+    auto configParameters = setupConfigParameters(commandLineArguments);
 
     return 0;
 }
diff --git a/dev/cmake/ConfigCatch2.cmake b/dev/cmake/ConfigCatch2.cmake
index 0e3cfb3..bab7daf 100644
--- a/dev/cmake/ConfigCatch2.cmake
+++ b/dev/cmake/ConfigCatch2.cmake
@@ -17,4 +17,5 @@
 #         "Path to Catch2 include directory" 
 #     FORCE)
 
-find_package(Catch2 REQUIRED)
\ No newline at end of file
+find_package(Catch2 REQUIRED)
+include_directories(${CATCH3_INCLUDE_DIRS})
\ No newline at end of file
diff --git a/dev/cmake/ConfigEigen.cmake b/dev/cmake/ConfigEigen.cmake
index 6e793ed..e4de143 100644
--- a/dev/cmake/ConfigEigen.cmake
+++ b/dev/cmake/ConfigEigen.cmake
@@ -13,4 +13,5 @@
 # # Optionally, include Armadillo headers if needed explicitly
 # include_directories(${ARMADILLO_INCLUDE_DIRS})
 
-find_package(Eigen3 REQUIRED)
\ No newline at end of file
+find_package(Eigen3 REQUIRED)
+include_directories(${EIGEN3_INCLUDE_DIRS})
\ No newline at end of file
diff --git a/dev/cmake/ConfigHDF5.cmake b/dev/cmake/ConfigHDF5.cmake
index 41ed2d1..908c824 100644
--- a/dev/cmake/ConfigHDF5.cmake
+++ b/dev/cmake/ConfigHDF5.cmake
@@ -16,5 +16,4 @@
 #    FORCE)
 
 find_package(HDF5 REQUIRED COMPONENTS C CXX)
-
 include_directories(${HDF5_INCLUDE_DIRS})
\ No newline at end of file
diff --git a/dev/cmake/ConfigYamlCpp.cmake b/dev/cmake/ConfigYamlCpp.cmake
index 28798db..fb5bc4c 100644
--- a/dev/cmake/ConfigYamlCpp.cmake
+++ b/dev/cmake/ConfigYamlCpp.cmake
@@ -27,4 +27,4 @@
 # # FetchContent_MakeAvailable(some_dependency)
 
 find_package(yaml-cpp REQUIRED)
-
+include_directories(${YAML_CPP_INCLUDE_DIRS})
\ No newline at end of file
diff --git a/dev/cmake/WriteIncludeDirs.cmake b/dev/cmake/WriteIncludeDirs.cmake
new file mode 100644
index 0000000..64c327f
--- /dev/null
+++ b/dev/cmake/WriteIncludeDirs.cmake
@@ -0,0 +1,13 @@
+# Get the list of include directories (e.g., target_include_directories or include_directories)
+get_property(INCLUDE_DIRS DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+
+# Specify the output file
+set(OUTPUT_FILE "${CMAKE_BINARY_DIR}/include_paths.txt")
+
+# Open the file for writing
+file(WRITE ${OUTPUT_FILE} "")
+
+# Iterate over the list of include directories and write each to the file
+foreach(INCLUDE_DIR ${INCLUDE_DIRS})
+    file(APPEND ${OUTPUT_FILE} "${INCLUDE_DIR}\n")
+endforeach()
\ No newline at end of file
diff --git a/dev/libs/CMakeLists.txt b/dev/libs/CMakeLists.txt
index 62975dc..f0fcacf 100644
--- a/dev/libs/CMakeLists.txt
+++ b/dev/libs/CMakeLists.txt
@@ -1,11 +1,8 @@
-# types
-add_subdirectory(types)
 
-# constants
-add_subdirectory(constants)
 
-# config
-add_subdirectory(data_processing)
 
-# electrons
-add_subdirectory(electrons)
+
+add_subdirectory(types)
+add_subdirectory(constants)
+add_subdirectory(data_processing)
+add_subdirectory(electrons)
\ No newline at end of file
diff --git a/dev/libs/constants/CMakeLists.txt b/dev/libs/constants/CMakeLists.txt
index 2320e0e..f8d48cf 100644
--- a/dev/libs/constants/CMakeLists.txt
+++ b/dev/libs/constants/CMakeLists.txt
@@ -2,6 +2,7 @@
 
 add_library(constants INTERFACE)
 
-target_include_directories(constants INTERFACE
-    include
+target_include_directories(constants 
+    INTERFACE
+        include
 )
\ No newline at end of file
diff --git a/dev/libs/data_processing/CMakeLists.txt b/dev/libs/data_processing/CMakeLists.txt
index 8230736..9793b59 100644
--- a/dev/libs/data_processing/CMakeLists.txt
+++ b/dev/libs/data_processing/CMakeLists.txt
@@ -12,7 +12,7 @@ target_link_libraries(data_processing
 
 target_include_directories(data_processing
         PUBLIC
-            ${CMAKE_SOURCE_DIR}/include
+            include
         PRIVATE
             src
 )
\ No newline at end of file
diff --git a/scripts/bash/clang-tidy.sh b/scripts/bash/clang-tidy.sh
index 20edddd..ff03c38 100644
--- a/scripts/bash/clang-tidy.sh
+++ b/scripts/bash/clang-tidy.sh
@@ -1,30 +1,50 @@
 #!/bin/bash
 
-PROJECT_DIR=$1
-COMPILE_COMMANDS=$2
+
+
+BUILD_DIR=$1
+SRC_DIR=$2
 CONFIG_FILE=$3
-SRC_DIR=$4
-CPP_STD=$5
-NUMBER_OF_ARGUMENTS=5
+CPP_STD=$4
 
 # Check if enough arguments are passed
+NUMBER_OF_ARGUMENTS=5
 if [ "$#" -ne ${NUMBER_OF_ARGUMENTS} ]; then
-    echo "Usage: $0 <project_dir> <compile_commands> <config_file> <src> <cpp_std>"
+    echo "Usage: $0 <BUILD_DIR> <SRC_DIR> <CONFIG_FILE> <CPP_STD> <INCLUDE_LIBS_EXT>"
     exit 1
 fi
 
-# Check if compile_commands.json exists
-if [ ! -f ${COMPILE_COMMANDS} ]; then
-    echo "${COMPILE_COMMANDS} not found!"
-    exit 1
-fi
+# Find compile_commands.json in build dir
+COMPILE_COMMANDS_FILE="compile_commands.json"
+INCLUDE_PATHS_EXT_FILE="include_paths.txt"
+BUILDS=$(find "${BUILD_DIR}" -maxdepth 1 -type d)
+COMPILE_COMMANDS=""
+INCLUDE_PATHS_EXT=()
+for BUILD in ${BUILDS}; do
+    if [ -d "${BUILD}" ]; then
+        COMPILE_COMMANDS="${BUILD}/${COMPILE_COMMANDS_FILE}"
+        mapfile -t INCLUDE_PATHS_EXT < "${BUILD}/${INCLUDE_PATHS_EXT_FILE}"
+        echo "Running clang-tidy with ${COMPILE_COMMANDS}..."
+    fi
+done
+if [ -z ${COMPILE_COMMANDS} ]; then\
+    echo "Could not find ${COMPILE_COMMANDS_FILE}. Exit..."
+    exit 
+fi 
+
 
 # Find all directories named "include" and generate the include string
-INCLUDE_PATHS=$(find "$PROJECT_DIR" -type d -name "include" -print | awk '{printf "-I%s ", $0}')
+INCLUDE_PATHS_INT=$(find "$SRC_DIR" -type d -name "include" -print)
+INCLUDE_PATHS_LIST=("${INCLUDE_PATHS_EXT[@]}" "${INCLUDE_PATHS_INT[@]}")
+INCLUDE_PATHS=""
+for LIB in ${INCLUDE_PATHS_LIST[@]}; do 
+    INCLUDE_PATHS+="-I${LIB} "
+done
+
 
 # Run clang-tidy for all cpp files
 for file in $(find ${SRC_DIR} -name '*.cpp'); do
     echo "Running clang-tidy on $file "
-    clang-tidy ${file} --config-file=${CONFIG_FILE} -- -std=${CPP_STD} ${INCLUDE_PATHS} "-I/usr/include/eigen3" "-I/usr/include/catch2"
+    clang-tidy ${file} --config-file=${CONFIG_FILE} -- -std=${CPP_STD} ${INCLUDE_PATHS} 
 
 done