vcs.xml file gets modified on branch switch and on Maven project reload

Problem

Sometimes when another git branch is checked out or a Maven project is reloaded, the vcs.xml file gets automatically modified and causes issues with the project's git integration.

Example of vcs.xml content before the branch switch/project reload:

<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
  <component name="VcsDirectoryMappings">
    <mapping directory="$PROJECT_DIR$" vcs="Git" />
  </component>
</project>

After the branch switch/project reload:

<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
  <component name="VcsDirectoryMappings">
    <mapping directory="" vcs="Git" />
  </component>
</project>

Resolution

Close IDE, delete .idea folder and any *.iml files in your project root folder in the file explorer, and re-import the project from existing sources. It will recreate the project configuration from scratch.

Note: If there is a lot of project-level configuration, it is recommended to move/backup the .idea folder instead of deleting it.