Filter libs with absolute paths

as the config system uses only abspaths

tools/config/__init__.py

@@ -1318,7 +1318,7 @@ class Config(object):
             ref for ref in resources.get_file_refs(FileType.JSON)
             if (
                 not ref.name.endswith(self.__mbed_lib_config_name)
-                or ref.path in all_json_paths
+                or abspath(ref.path) in all_json_paths
             )
         ]
         resources.filter_by_libraries(included_json_files)