Get an eclipse project. Specify some source root (e.g. "src"). In project properties provide native library location and alternate output folder (such eclipse options) for this source root. Import eclipse project to IDEA module. Choose to use .classpath file. Result: after opening in IDEA mentioned settings are erased from .classpath file. It may be Ok not to import these settings, but they should not be erased. UPDATE: same for access rules to dependent project eclipse setting.