diff --git a/CMakeLists.txt b/CMakeLists.txt
index 831a1053..a8049ab3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -31,51 +31,55 @@ if(AARE_BUILD_TESTS)
     add_subdirectory(tests)
 endif()
 
-
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 find_package(fmt 6 REQUIRED)
 
 
-set(CMAKE_BUILD_TYPE "Debug")
+# set(CMAKE_BUILD_TYPE "Debug")
 
-if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-    set(OPTIMIZATION_FLAGS "-Og -ggdb3 -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC")
-else()
-    set(OPTIMIZATION_FLAGS "-O3")
-endif()
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+# if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+#     set(OPTIMIZATION_FLAGS "-Og -ggdb3 -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC")
+# else()
+#     set(OPTIMIZATION_FLAGS "-O3")
+# endif()
 
 
 
 
-set(OPTIONAL_FLAGS "")
-if(DISABLE_WARNINGS)
-    set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -Wall -Wextra -pedantic -Wno-unused-parameter -Wshadow -Wformat=2 -Wold-style-cast -Wnon-virtual-dtor  -Wfloat-equal -Wconversion -Wlogical-op -Wshift-overflow=2 -Woverloaded-virtual -Winline")
-endif()
 
-if(USE_SANITIZER)
-    set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -fdiagnostics-parseable-fixits -fdiagnostics-generate-patch -fdiagnostics-show-template-tree -fsanitize=address,undefined,pointer-compare -fno-sanitize-recover -D_FORTIFY_SOURCE=2 -fstack-protector -fno-omit-frame-pointer ")
-endif()
+# set(OPTIONAL_FLAGS "")
+# if(DISABLE_WARNINGS)
+#     set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -Wall -Wextra -pedantic -Wno-unused-parameter -Wshadow -Wformat=2 -Wold-style-cast -Wnon-virtual-dtor  -Wfloat-equal -Wconversion -Wlogical-op -Wshift-overflow=2 -Woverloaded-virtual -Winline")
+# endif()
 
+# if(USE_SANITIZER)
+#     set(OPTIONAL_FLAGS "${OPTIONAL_FLAGS} -fdiagnostics-parseable-fixits -fdiagnostics-generate-patch -fdiagnostics-show-template-tree -fsanitize=address,undefined,pointer-compare -fno-sanitize-recover -D_FORTIFY_SOURCE=2 -fstack-protector -fno-omit-frame-pointer ")
+# endif()
 
 
-set(SUPPRESSED_WARNINGS "-Wno-return-type")
 
-set(CMAKE_CXX_FLAGS  "${OPTIMIZATION_FLAGS} ${SUPPRESSED_WARNINGS}")
+# set(SUPPRESSED_WARNINGS "-Wno-return-type")
+
+# set(CMAKE_CXX_FLAGS  "${OPTIMIZATION_FLAGS} ${SUPPRESSED_WARNINGS}")
+
+# if(USE_PYTHON)
+# set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -fPIC")
+# endif(USE_PYTHON)
+
 
-if(USE_PYTHON)
-set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -fPIC")
-endif(USE_PYTHON)
 
 
+# include_directories(include)
+# add_subdirectory(src)
 
+add_subdirectory(core)
+add_subdirectory(file_io)
 
-include_directories(include)
-add_subdirectory(src)
 
 
 add_library(aare INTERFACE) 
-target_link_libraries(aare INTERFACE common core file_io)
+target_link_libraries(aare INTERFACE core file_io)
 
 
 add_subdirectory(examples)
diff --git a/README.md b/README.md
index 46b0ba75..1b317695 100644
--- a/README.md
+++ b/README.md
@@ -4,5 +4,13 @@ Data analysis library for PSI hybrid detectors
 
 
 
+## Folder structure 
+
+| Folder   | subfolder     | Content                             |
+|----------|---------------|-------------------------------------|
+| include/ |  aare/        | top level header/s                  |
+| core/    |    include/   | public headers for core             |
+|          | src/          | source files and non public headers |
+
 ## file_io class diagram
 ![file_io class diagram](./extra/uml/out/file_io/ClassDiagram.png)
\ No newline at end of file
diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
new file mode 100644
index 00000000..35d808d0
--- /dev/null
+++ b/core/CMakeLists.txt
@@ -0,0 +1,23 @@
+
+
+set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
+)
+
+add_library(core STATIC ${SourceFiles})
+target_include_directories(core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+target_link_libraries(core PUBLIC fmt::fmt)
+set_property(TARGET core PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+if(AARE_BUILD_TESTS)
+    set(TestSources
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+        )
+    target_sources(tests PRIVATE ${TestSources} )
+
+    #Work around to remove, this is not the way to do it =) 
+    # target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common)
+    target_link_libraries(tests PRIVATE core)
+
+endif()
diff --git a/include/core/Frame.hpp b/core/include/aare/Frame.hpp
similarity index 96%
rename from include/core/Frame.hpp
rename to core/include/aare/Frame.hpp
index 902806da..78918a6c 100644
--- a/include/core/Frame.hpp
+++ b/core/include/aare/Frame.hpp
@@ -4,7 +4,7 @@
 #include <cstdint>
 #include <bits/unique_ptr.h>
 #include <vector>
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 
 
 
diff --git a/include/common/defs.hpp b/core/include/aare/defs.hpp
similarity index 100%
rename from include/common/defs.hpp
rename to core/include/aare/defs.hpp
diff --git a/src/core/Frame.cpp b/core/src/Frame.cpp
similarity index 95%
rename from src/core/Frame.cpp
rename to core/src/Frame.cpp
index 9af474d8..f035fc4e 100644
--- a/src/core/Frame.cpp
+++ b/core/src/Frame.cpp
@@ -1,4 +1,4 @@
-#include "core/Frame.hpp"
+#include "aare/Frame.hpp"
 #include <iostream>
 
 template <typename DataType>
diff --git a/src/common/defs.cpp b/core/src/defs.cpp
similarity index 97%
rename from src/common/defs.cpp
rename to core/src/defs.cpp
index a6ba4582..dea1f851 100644
--- a/src/common/defs.cpp
+++ b/core/src/defs.cpp
@@ -1,4 +1,4 @@
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 
 template <> std::string toString(DetectorType type) {
     switch (type) {
diff --git a/src/common/defs.test.cpp b/core/src/defs.test.cpp
similarity index 92%
rename from src/common/defs.test.cpp
rename to core/src/defs.test.cpp
index 4e5caf71..ecad6829 100644
--- a/src/common/defs.test.cpp
+++ b/core/src/defs.test.cpp
@@ -1,6 +1,6 @@
 #include <catch2/catch_test_macros.hpp>
 #include <string>
-#include "defs.hpp"
+#include "aare/defs.hpp"
 TEST_CASE("Enum to string conversion"){
     //By the way I don't think the enum string conversions should be in the defs.hpp file
     //but let's use this to show a test
diff --git a/examples/main.cpp b/examples/main.cpp
index 693cabea..f4d45cb8 100644
--- a/examples/main.cpp
+++ b/examples/main.cpp
@@ -1,6 +1,6 @@
 // Your First C++ Program
 #include <iostream>
-#include "file_io/FileHandler.hpp"
+#include "aare/FileHandler.hpp"
 
 using JFileHandler = FileHandler<DetectorType::Jungfrau,uint16_t>;
 using JFile = File<DetectorType::Jungfrau,uint16_t>;
diff --git a/file_io/CMakeLists.txt b/file_io/CMakeLists.txt
new file mode 100644
index 00000000..ff9bc562
--- /dev/null
+++ b/file_io/CMakeLists.txt
@@ -0,0 +1,28 @@
+
+
+set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/FileFactory.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/helpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/JsonFileFactory.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/SubFile.cpp
+)
+
+add_library(file_io STATIC ${SourceFiles})
+target_include_directories(file_io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+target_link_libraries(file_io  PUBLIC fmt::fmt core nlohmann_json::nlohmann_json)
+set_property(TARGET file_io PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+
+# if(AARE_BUILD_TESTS)
+#     set(TestSources
+#             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+#         )
+#     target_sources(tests PRIVATE ${TestSources} )
+
+#     #Work around to remove, this is not the way to do it =) 
+#     # target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common)
+#     target_link_libraries(tests PRIVATE file_io)
+
+# endif()
diff --git a/include/file_io/File.hpp b/file_io/include/aare/File.hpp
similarity index 97%
rename from include/file_io/File.hpp
rename to file_io/include/aare/File.hpp
index 01239a51..a30e7c8d 100644
--- a/include/file_io/File.hpp
+++ b/file_io/include/aare/File.hpp
@@ -1,8 +1,9 @@
 #pragma once
 
-#include "common/defs.hpp"
-#include "core/Frame.hpp"
+#include "aare/defs.hpp"
+#include "aare/Frame.hpp"
 #include "SubFile.hpp"
+
 #include <filesystem>
 #include <fmt/core.h>
 #include <iostream>
diff --git a/include/file_io/FileFactory.hpp b/file_io/include/aare/FileFactory.hpp
similarity index 96%
rename from include/file_io/FileFactory.hpp
rename to file_io/include/aare/FileFactory.hpp
index 1b89f3c3..abb583d0 100644
--- a/include/file_io/FileFactory.hpp
+++ b/file_io/include/aare/FileFactory.hpp
@@ -1,6 +1,7 @@
 #pragma once
 #include <filesystem>
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector,typename DataType>
 class FileFactory{
     // Class that will be used to create File objects
diff --git a/include/file_io/FileHandler.hpp b/file_io/include/aare/FileHandler.hpp
similarity index 90%
rename from include/file_io/FileHandler.hpp
rename to file_io/include/aare/FileHandler.hpp
index afe459d2..c28e6819 100644
--- a/include/file_io/FileHandler.hpp
+++ b/file_io/include/aare/FileHandler.hpp
@@ -1,6 +1,7 @@
 #include <filesystem>
-#include "file_io/FileFactory.hpp"
-#include "file_io/File.hpp"
+#include "aare/FileFactory.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector,typename DataType>
 class FileHandler{
     private:
diff --git a/include/file_io/JsonFile.hpp b/file_io/include/aare/JsonFile.hpp
similarity index 67%
rename from include/file_io/JsonFile.hpp
rename to file_io/include/aare/JsonFile.hpp
index d3ae890f..b82aebc3 100644
--- a/include/file_io/JsonFile.hpp
+++ b/file_io/include/aare/JsonFile.hpp
@@ -1,7 +1,7 @@
 #pragma once
-#include "file_io/File.hpp"
-#include "core/Frame.hpp"
-#include "common/defs.hpp"
+#include "aare/File.hpp"
+#include "aare/Frame.hpp"
+#include "aare/defs.hpp"
 template <DetectorType detector, typename DataType>
 class JsonFile : public File<detector, DataType> {
 
diff --git a/include/file_io/JsonFileFactory.hpp b/file_io/include/aare/JsonFileFactory.hpp
similarity index 91%
rename from include/file_io/JsonFileFactory.hpp
rename to file_io/include/aare/JsonFileFactory.hpp
index 347baf49..cdbfb95a 100644
--- a/include/file_io/JsonFileFactory.hpp
+++ b/file_io/include/aare/JsonFileFactory.hpp
@@ -1,4 +1,4 @@
-#include "file_io/FileFactory.hpp"
+#include "aare/FileFactory.hpp"
 template <DetectorType detector,typename DataType>
 class JsonFileFactory: public FileFactory<detector,DataType>
 {
diff --git a/include/file_io/RawFileFactory.hpp b/file_io/include/aare/RawFileFactory.hpp
similarity index 89%
rename from include/file_io/RawFileFactory.hpp
rename to file_io/include/aare/RawFileFactory.hpp
index 15877cc2..66a3f590 100644
--- a/include/file_io/RawFileFactory.hpp
+++ b/file_io/include/aare/RawFileFactory.hpp
@@ -1,4 +1,4 @@
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
 #include <filesystem>
 template<DetectorType detector,typename DataType>  
 class RawFileFactory{
diff --git a/include/file_io/SubFile.hpp b/file_io/include/aare/SubFile.hpp
similarity index 97%
rename from include/file_io/SubFile.hpp
rename to file_io/include/aare/SubFile.hpp
index fd9b87c7..02efa39a 100644
--- a/include/file_io/SubFile.hpp
+++ b/file_io/include/aare/SubFile.hpp
@@ -1,5 +1,5 @@
 #pragma once
-#include "common/defs.hpp"
+#include "aare/defs.hpp"
 #include <cstdint>
 #include <filesystem>
 #include <variant>
diff --git a/include/file_io/helpers.hpp b/file_io/include/aare/helpers.hpp
similarity index 79%
rename from include/file_io/helpers.hpp
rename to file_io/include/aare/helpers.hpp
index 199e6acb..a140f58a 100644
--- a/include/file_io/helpers.hpp
+++ b/file_io/include/aare/helpers.hpp
@@ -1,6 +1,6 @@
 #pragma once
 
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
 #include <filesystem>
 #include <fmt/core.h>
 
diff --git a/src/file_io/file/File.cpp b/file_io/src/File.cpp
similarity index 89%
rename from src/file_io/file/File.cpp
rename to file_io/src/File.cpp
index 9ee20c31..9cebbcc6 100644
--- a/src/file_io/file/File.cpp
+++ b/file_io/src/File.cpp
@@ -1,4 +1,5 @@
-#include "file_io/File.hpp"
+#include "aare/File.hpp"
+
 template <DetectorType detector, typename DataType>
 File<detector,DataType>::~File<detector,DataType>() {
     for (auto& subfile : subfiles) {
diff --git a/src/file_io/file_factory/FileFactory.cpp b/file_io/src/FileFactory.cpp
similarity index 96%
rename from src/file_io/file_factory/FileFactory.cpp
rename to file_io/src/FileFactory.cpp
index 5a5d4657..d56e14ce 100644
--- a/src/file_io/file_factory/FileFactory.cpp
+++ b/file_io/src/FileFactory.cpp
@@ -1,6 +1,6 @@
-#include "file_io/FileFactory.hpp"
-#include "file_io/File.hpp"
-#include "file_io/JsonFileFactory.hpp"
+#include "aare/FileFactory.hpp"
+#include "aare/File.hpp"
+#include "aare/JsonFileFactory.hpp"
 #include <iostream>
 
 template <DetectorType detector, typename DataType>
diff --git a/src/file_io/file/JsonFile.cpp b/file_io/src/JsonFile.cpp
similarity index 94%
rename from src/file_io/file/JsonFile.cpp
rename to file_io/src/JsonFile.cpp
index 7c0a31e2..0d848d9a 100644
--- a/src/file_io/file/JsonFile.cpp
+++ b/file_io/src/JsonFile.cpp
@@ -1,4 +1,4 @@
-#include "file_io/JsonFile.hpp"
+#include "aare/JsonFile.hpp"
 #include <typeinfo>
 
 template <DetectorType detector, typename DataType>
diff --git a/src/file_io/file_factory/JsonFileFactory.cpp b/file_io/src/JsonFileFactory.cpp
similarity index 94%
rename from src/file_io/file_factory/JsonFileFactory.cpp
rename to file_io/src/JsonFileFactory.cpp
index 843dcf92..c8a6f611 100644
--- a/src/file_io/file_factory/JsonFileFactory.cpp
+++ b/file_io/src/JsonFileFactory.cpp
@@ -1,8 +1,8 @@
-#include "file_io/JsonFileFactory.hpp"
-#include "file_io/JsonFile.hpp"
-#include "file_io/SubFile.hpp"
-#include "common/defs.hpp"
-#include "file_io/helpers.hpp"
+#include "aare/JsonFileFactory.hpp"
+#include "aare/JsonFile.hpp"
+#include "aare/SubFile.hpp"
+#include "aare/defs.hpp"
+#include "aare/helpers.hpp"
 #include <fstream>
 #include <iostream>
 #include <nlohmann/json.hpp>
diff --git a/src/file_io/file/SubFile.cpp b/file_io/src/SubFile.cpp
similarity index 99%
rename from src/file_io/file/SubFile.cpp
rename to file_io/src/SubFile.cpp
index 08875dcc..7b3ac1d8 100644
--- a/src/file_io/file/SubFile.cpp
+++ b/file_io/src/SubFile.cpp
@@ -1,4 +1,4 @@
-#include "file_io/SubFile.hpp"
+#include "aare/SubFile.hpp"
 #include <iostream>
 // #include <filesystem>
 
diff --git a/src/file_io/helpers.cpp b/file_io/src/helpers.cpp
similarity index 86%
rename from src/file_io/helpers.cpp
rename to file_io/src/helpers.cpp
index d16f8be7..9c7ceeb8 100644
--- a/src/file_io/helpers.cpp
+++ b/file_io/src/helpers.cpp
@@ -1,4 +1,4 @@
-#include "file_io/helpers.hpp"
+#include "aare/helpers.hpp"
 
 
 bool is_master_file(std::filesystem::path fpath) {
diff --git a/include/aare/aare.hpp b/include/aare/aare.hpp
new file mode 100644
index 00000000..6734b06d
--- /dev/null
+++ b/include/aare/aare.hpp
@@ -0,0 +1 @@
+//This is the top level header to include and what most users will use
\ No newline at end of file
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 33272733..18d1b173 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -1 +1,4 @@
 pybind11_add_module(_aare src/bindings.cpp)
+set_target_properties(_aare PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+)
\ No newline at end of file
diff --git a/python/src/bindings.cpp b/python/src/bindings.cpp
index 249323df..ab861fe5 100644
--- a/python/src/bindings.cpp
+++ b/python/src/bindings.cpp
@@ -3,9 +3,9 @@
 #include <pybind11/pybind11.h>
 #include <string>
 
-#include "common/defs.hpp"
-#include "core/Frame.hpp"
-#include "file_io/FileHandler.hpp"
+#include "aare/defs.hpp"
+#include "aare/Frame.hpp"
+#include "aare/FileHandler.hpp"
 
 namespace py = pybind11;
 
diff --git a/src/.gitignore b/src/.gitignore
deleted file mode 100644
index 8b137891..00000000
--- a/src/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
deleted file mode 100644
index 99386b50..00000000
--- a/src/CMakeLists.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-add_subdirectory(file_io)
-add_subdirectory(core)
-add_subdirectory(processing)
-add_subdirectory(common)
diff --git a/src/common/CMakeLists.txt b/src/common/CMakeLists.txt
deleted file mode 100644
index aedc0336..00000000
--- a/src/common/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-add_library(common "${CMAKE_CURRENT_SOURCE_DIR}/defs.cpp")
-
-target_link_libraries(common PUBLIC fmt::fmt)
-
-
-if(AARE_BUILD_TESTS)
-    set(TestSources
-            ${CMAKE_CURRENT_SOURCE_DIR}/defs.test.cpp
-        )
-    target_sources(tests PRIVATE ${TestSources} )
-
-    #Work around to remove, this is not the way to do it =) 
-    target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common)
-    target_link_libraries(tests PRIVATE common)
-
-endif()
\ No newline at end of file
diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
deleted file mode 100644
index 7c3061eb..00000000
--- a/src/core/CMakeLists.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-# target_include_directories(aare PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-
-# target_sources(aare PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/Frame.cpp")
-
-
-add_library(core "${CMAKE_CURRENT_SOURCE_DIR}/Frame.cpp")
-
-target_link_libraries(core PUBLIC common)
-
-
diff --git a/src/file_io/CMakeLists.txt b/src/file_io/CMakeLists.txt
deleted file mode 100644
index 72e5adc0..00000000
--- a/src/file_io/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-
-set(FILE_IO_SOURCES "file/File.cpp"
-                    "file/JsonFile.cpp"
-                    "file/SubFile.cpp"
-                    "file_factory/FileFactory.cpp"
-                    "file_factory/JsonFileFactory.cpp"
-                    "helpers.cpp"
-                    )
-# append ${CMAKE_CURRENT_SOURCE_DIR} to the list of sources using for loop
-foreach(FILE_IO_SOURCE ${FILE_IO_SOURCES})
-    list(APPEND FILE_IO_SOURCES_WITH_PATH "${CMAKE_CURRENT_SOURCE_DIR}/${FILE_IO_SOURCE}")
-endforeach()
-
-add_library(file_io ${FILE_IO_SOURCES_WITH_PATH})
-
-target_link_libraries(file_io common fmt::fmt core nlohmann_json::nlohmann_json)
\ No newline at end of file
diff --git a/src/processing/CMakeLists.txt b/src/processing/CMakeLists.txt
deleted file mode 100644
index e69de29b..00000000
diff --git a/tests/.gitignore b/tests/.gitignore
deleted file mode 100644
index 8b137891..00000000
--- a/tests/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-