When using --with-java-path we should probably execute this early on, in the EARLY custom hook. And we should set like DEFAULT_FREETYPE, DEFAULT_TOOLS_DIR, etc. And then we should check for the presence of these defaults in the open files when setting freetype, tools-dir, etc. And if they are available, we should use them instead and notify the user that the default has been overridden due to --with-java-path. (But if we change default for freetype but don't need freetype, we should not complain).