diff --git a/Makefile b/Makefile
index c8585e3..eb70560 100644
--- a/Makefile
+++ b/Makefile
@@ -8,8 +8,10 @@ BUILD_DIR := ${PWD}/build
 SRC_DIR := ${PWD}/src
 FLATPAK_STATE_DIR := ${PWD}/flatpak-state
 FLATPAK_CACHE_DIR := ${PWD}/flatpak-cache
-# Whether to use a clean build each time (set to empty to disable)
-# CLEAN_BUILD := --force-clean
+
+# Get current user and group IDs to avoid permission issues with Docker
+USER_ID := $(shell id -u)
+GROUP_ID := $(shell id -g)
 
 # --- Main Targets ---
 # Default target
@@ -20,7 +22,8 @@ all: build
 .PHONY: prepare-sources
 prepare-sources:
 	@echo "--- Preparing sources using prepare_sources.sh ---"
-	@./prepare_sources.sh
+	./prepare_sources.sh
+	./prepare_sources.sh --check-integrity
 
 # Build the Docker image which runs flatpak-builder inside
 # Implicitly depends on sources being ready after prepare-sources runs
@@ -29,8 +32,7 @@ build-image:
 	@echo "--- Building Aseprite Flatpak builder image (${IMAGE_NAME}) ---"
 	@docker build -t ${IMAGE_NAME} -f ${DOCKERFILE} .
 
-# Run flatpak-builder inside a privileged container
-# Create persistent cache directories to improve caching
+# Run flatpak-builder inside a privileged container with proper user permissions
 .PHONY: run-flatpak-builder
 run-flatpak-builder:
 	@echo "--- Running flatpak-builder inside container ---"
@@ -44,9 +46,12 @@ run-flatpak-builder:
 	-v ${FLATPAK_STATE_DIR}:/root/.local/share/flatpak-builder \
 	-v ${FLATPAK_CACHE_DIR}:/root/.cache/flatpak-builder \
 	-v ${PWD}/com.aseprite.Aseprite.yaml:/build/com.aseprite.Aseprite.yaml:ro \
+	-e FLATPAK_USER_DIR=/build/.flatpak \
+	-e USER_ID=${USER_ID} \
+	-e GROUP_ID=${GROUP_ID} \
 	-w /build \
 	${IMAGE_NAME} \
-	sh -c "flatpak-builder --disable-rofiles-fuse --state-dir=/root/.local/share/flatpak-builder --ccache ${CLEAN_BUILD} build-dir com.aseprite.Aseprite.yaml --repo=repo && if [ -d 'build-dir/files/third_party/externals/emsdk' ]; then rm -rf build-dir/files/third_party/externals/emsdk; fi"
+	sh -c "flatpak-builder --disable-rofiles-fuse --state-dir=/root/.local/share/flatpak-builder --ccache build-dir com.aseprite.Aseprite.yaml --repo=repo && if [ -d 'build-dir/files/third_party/externals/emsdk' ]; then rm -rf build-dir/files/third_party/externals/emsdk; fi && chown -R ${USER_ID}:${GROUP_ID} /build"
 
 # Create the Flatpak bundle from the repo built in the previous step
 .PHONY: create-bundle
@@ -57,9 +62,11 @@ create-bundle: run-flatpak-builder
 	--privileged \
 	--device /dev/fuse \
 	-v ${BUILD_DIR}:/build \
+	-e USER_ID=${USER_ID} \
+	-e GROUP_ID=${GROUP_ID} \
 	-w /build \
 	${IMAGE_NAME} \
-	sh -c "flatpak build-bundle repo aseprite.flatpak com.aseprite.Aseprite"
+	sh -c "flatpak build-bundle repo aseprite.flatpak com.aseprite.Aseprite && chown ${USER_ID}:${GROUP_ID} aseprite.flatpak"
 
 # Copy the final bundle from the intermediate directory to the output directory
 .PHONY: extract-flatpak
@@ -79,24 +86,9 @@ prepare: prepare-sources build-image
 build: run-flatpak-builder create-bundle extract-flatpak
 	@echo "--- Build complete ---"
 
-# --- Utility Targets ---
-# Clean up the output and intermediate build directories
+# Clean up only the source files and downloaded content
 .PHONY: clean
 clean:
-	@echo "--- Cleaning up ---"
-	@rm -rf ${TARGET_DIR}
-	@rm -rf ${BUILD_DIR}
-	@echo "Cleanup complete."
-
-# Deep clean - removes all caches as well
-.PHONY: deep-clean
-deep-clean: clean
-	@echo "--- Deep cleaning (including caches) ---"
-	@rm -rf ${FLATPAK_STATE_DIR}
-	@rm -rf ${FLATPAK_CACHE_DIR}
-	@echo "Deep cleanup complete."
-
-# Force clean build by setting CLEAN_BUILD variable
-.PHONY: force-clean-build
-force-clean-build:
-	@$(MAKE) CLEAN_BUILD="--force-clean" build
+	@echo "--- Cleaning source files ---"
+	@rm -rf ${SRC_DIR}
+	@echo "Source files cleaned. Run 'prepare-sources' to download them again."