I missed this one
@@ -105,7 +105,7 @@ board = at90usb1286
build_flags = ${common.build_flags}
lib_deps = ${common.lib_deps}
lib_ldf_mode = deep+
-src_filter = ${common.default_src_filter}
+src_filter = ${common.default_src_filter} +<src/HAL/HAL_AVR>
extra_scripts = pre:buildroot/share/atom/create_custom_upload_command_DFU.py
monitor_speed = 250000