Get rid of `clang-tidy.cmake` as it is not present in cmake installation.
Change SQLite3's `find_package` to `REQUIRED` as the `sqlite3` package does not provide a .cmake file, so we fall back to cmake's included definition.
We change the install directory to the store output rather than /usr. `@OUTPUT_DIR@` is substituted to the store path in an added phase.
For the /data and /user directories, we move them to /share/sourcetrail rather than leaving them in the /bin directory.

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b8b91d9c..d5dbdfa2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -69,7 +69,6 @@ include(cmake/create_symlink.cmake)
 include(cmake/add_sourcetrail_library.cmake)
 include(cmake/add_sourcetrail_interface.cmake)
 include(cmake/add_sourcetrail_test.cmake)
-include(cmake/clang-tidy.cmake)
 include(cmake/cppcheck.cmake)
 include(cmake/coverage.cmake)
 #---------------------------------------------------------------------------------------------------------------------------------
@@ -142,12 +141,9 @@ find_package(expected-lite REQUIRED)
 find_package(fmt CONFIG REQUIRED)
 find_package(range-v3 CONFIG REQUIRED)
 find_package(spdlog CONFIG REQUIRED)
-find_package(SQLite3 CONFIG REQUIRED)
+find_package(SQLite3 REQUIRED)
 # Boost --------------------------------------------------------------------------------------------------------------------------
 set(Boost_USE_MULTITHREAD ON)
-set(Boost_USE_STATIC_LIBS
-    ON
-    CACHE BOOL "Set to ON to force the use of the static libraries.")
 set(Boost_USE_STATIC_RUNTIME OFF)
 find_package(
   Boost 1.83
@@ -384,14 +380,14 @@ execute_process(COMMAND "${CMAKE_COMMAND}" "-E" "make_directory" "${CMAKE_BINARY
 create_symlink("${CMAKE_SOURCE_DIR}/bin/app/data" "${CMAKE_BINARY_DIR}/app/data")
 create_symlink("${CMAKE_SOURCE_DIR}/bin/app/user" "${CMAKE_BINARY_DIR}/app/user")
 # Install Executables ------------------------------------------------------------------------------------------------------------
-set(APPIMAGE_ROOT "usr")
+set(APPIMAGE_ROOT "@OUTPUT_DIR@")
 set(INSTALL_RUNTIME_DIR "${APPIMAGE_ROOT}/bin")
 
 install(TARGETS Sourcetrail Sourcetrail_indexer RUNTIME DESTINATION ${INSTALL_RUNTIME_DIR})
 
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/bin/app/data/ DESTINATION ${INSTALL_RUNTIME_DIR}/data/)
+install(DIRECTORY ${CMAKE_SOURCE_DIR}/bin/app/data/ DESTINATION ${APPIMAGE_ROOT}/share/sourcetrail/data/)
 
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/bin/app/user/ DESTINATION ${INSTALL_RUNTIME_DIR}/user/)
+install(DIRECTORY ${CMAKE_SOURCE_DIR}/bin/app/user/ DESTINATION ${APPIMAGE_ROOT}/share/sourcetrail/user/)
 
 # Install desktop file for application
 install(FILES "${CMAKE_SOURCE_DIR}/cmake/Sourcetrail.desktop" DESTINATION "${APPIMAGE_ROOT}/share/applications")

We remove the sample projects from the default `ApplicationSettings.xml` as they do not function properly, requiring their installed directory to be mutable,
which is not possible in the store. They are installed in the `projects` package output.

Submodule bin contains modified content
diff --git a/bin/app/data/fallback/ApplicationSettings.xml b/bin/app/data/fallback/ApplicationSettings.xml
index c1d3a78..33cf7d4 100644
--- a/bin/app/data/fallback/ApplicationSettings.xml
+++ b/bin/app/data/fallback/ApplicationSettings.xml
@@ -9,10 +9,6 @@
 	</indexing>
 	<user>
 		<recent_projects>
-			<recent_project>./projects/tutorial/tutorial.srctrlprj</recent_project>
-			<recent_project>./projects/tictactoe_cpp/tictactoe_cpp.srctrlprj</recent_project>
-			<recent_project>./projects/tictactoe_py/tictactoe_py.srctrlprj</recent_project>
-			<recent_project>./projects/javaparser/javaparser.srctrlprj</recent_project>
 		</recent_projects>
 	</user>
     <version>8</version>
diff --git a/bin/app/user/ApplicationSettings.xml b/bin/app/user/ApplicationSettings.xml
index 7081ab0..755281f 100755
--- a/bin/app/user/ApplicationSettings.xml
+++ b/bin/app/user/ApplicationSettings.xml
@@ -22,10 +22,6 @@
     </indexing>
     <user>
         <recent_projects>
-            <recent_project>C:/Hard/SourceCode/Sourcetrail/build/x64-Debug/Debug/app/user/./projects/tutorial/tutorial.srctrlprj</recent_project>
-            <recent_project>C:/Hard/SourceCode/Sourcetrail/build/x64-Debug/Debug/app/user/./projects/tictactoe_cpp/tictactoe_cpp.srctrlprj</recent_project>
-            <recent_project>C:/Hard/SourceCode/Sourcetrail/build/x64-Debug/Debug/app/user/./projects/tictactoe_py/tictactoe_py.srctrlprj</recent_project>
-            <recent_project>C:/Hard/SourceCode/Sourcetrail/build/x64-Debug/Debug/app/user/./projects/javaparser/javaparser.srctrlprj</recent_project>
         </recent_projects>
     </user>
     <version>8</version>

Set paths to /share/sourcetrail.

diff --git a/src/lib_gui/platform_includes/includesLinux.h b/src/lib_gui/platform_includes/includesLinux.h
index 79e8be7f..5dadcca5 100644
--- a/src/lib_gui/platform_includes/includesLinux.h
+++ b/src/lib_gui/platform_includes/includesLinux.h
@@ -43,6 +43,6 @@ inline void setupApp([[maybe_unused]] int argc, [[maybe_unused]] char* argv[]) {
   AppPath::setCxxIndexerDirectoryPath(appPath);
 
   // Check if bundled as Linux AppImage
-  if(appPath.getConcatenated(L"/../share/data").exists()) {
-    AppPath::setSharedDataDirectoryPath(appPath.getConcatenated(L"/../share").getAbsolute());
+  if(appPath.getConcatenated(L"/../share/sourcetrail/data").exists()) {
+    AppPath::setSharedDataDirectoryPath(appPath.getConcatenated(L"/../share/sourcetrail").getAbsolute());
   }