Clean up build system and update documentation

- Updated README.md to reflect current single-stage build architecture
- Removed obsolete scripts/build-boot.sh (unused two-stage boot approach)
- Updated cleanup.sh to remove reference to non-existent setup-submodules.sh
- Documented smart caching and component compilation workflow
- Added proper build variants (minimal vs full) documentation

scripts/cleanup.sh

@@ -176,5 +176,4 @@ echo "[+] Cleanup completed successfully!"
 echo ""
 echo "To rebuild the project after cleanup:"
 echo "  1. Run: ./build.sh                    # Full rebuild"
-echo "  2. Or:  docker-compose up --build     # Docker rebuild"
-echo "  3. Or:  scripts/setup-submodules.sh   # Restore submodules first"
+echo "  2. Or:  cd build && docker-compose up --build     # Docker rebuild"