This project for eclipse IDE enables you to reset certain config files:
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.classpath
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.project
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org.eclipse.wst.common.component
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org.eclipse.jdt.core.prefs
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org.eclipse.core.resources.prefs
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org.eclipse.wst.common.project.facet.core.xml
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org.eclipse.wst.validation.prefs
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org.eclipse.wst.common.project.facet.core.prefs.xml
Works with multiple selected repositories.
Build the fragment and copy the .jar file into /dropins of your eclipse installation. Restart the IDE. You should see a thumbs up icon in the "Git Repositories" view toolbar in the Git perspective.