Git plugin sees unattended changed files

[Former user]

Depuis https://git.eclipse.org/r/sirius/org.eclipse.sirius b5adcd9..089ecb9 master -> origin/master b1c1fbf..422ae26 v5.0.x -> origin/v5.0.x

error: Your local changes to the following files would be overwritten by merge: plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/interpreter/JavaExtensionsManager.java plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/internal/ecore/EPackageHelper.java

error: The following untracked working tree files would be removed by merge: plugins/org.eclipse.sirius.diagram.ui/src-diag/org/eclipse/sirius/diagram/ui/tools/internal/ui/GMFRuntimeCompatibility.java plugins/org.eclipse.sirius.ui.editor/src/org/eclipse/sirius/ui/editor/ModelCommonDropAdapterAssistant.java Please move or remove them before you can merge. Aborting at /home/boris/Projects/bb_alambic/mojo/bin/../lib/Alambic/Tools/Git.pm line 283.

[Boris Baldassari]

Happens only when messing up with files on filesystem. This is not recommended anyway. If than happens, recommended way is to delete the git repository in projects/<project.id>/src/ so it is recreated. Going to resolve.