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I noticed for some projects if they move things around, or unversion meta-data files I often get error messages when switching branches like this: Problems occurred while refreshing local changes Problems occurred while refreshing local changes Errors occurred while refreshing resources with the local file system. The project description file (.project) for 'org.eclipse.jdt.compiler.apt' is missing. This file contains important information about the project. The project will not function properly until this file is restored. The project description file (.project) for 'org.eclipse.jdt.compiler.apt' is missing. This file contains important information about the project. The project will not function properly until this file is restored. This can happen for example in the following case: 1) you have a branch where project files are checked in 2) you have a branch where files are not checked in If you switch between those it happens that git removes the project file an afterwards one ends up with a broken workspace, need to remove the project manually and import the project again so eclipse creates the .project file again. It would be good if egit could retain files required by eclipse of projects that are currently imported in the workspace (maybe mark them as "assume unchanged, keep them as unversioned, or whatever suffice), that should include .project .settings .classpath