A really annoying thing keeps happening whenver I change branch with a git checkout - IDEA puts all my Maven module pom.xml files into a <option name="ignoredFiles"> element in .idea/misc.xml, so all modules disappear from the project. I have to manually remove this section from misc.xml. Normally I do the git checkout on command line as there are a few glitches in IDEA's git integration. I think it also happens if I git checkout within IDEA - I can verify this if this is not a known issue and you need me to. Is there a workaround, and should I raise this as a bug?