There is experimental native (faster) file watching support which is
disabled by default.  Currently there are problems with watching large
trees.  To enable edit %%IDEA_HOME%%/bin/idea.properties and append

      idea.filewatcher.disabled=false
      idea.filewatcher.executable.path=%%IDEA_HOME%%/bin/fsnotifier

Only enable fsnotifier if your projects have < 600 files.

At systems which use links for /usr/home/user or /home/user apparently
IDEA finds two different VCS roots while trying to integrate with Git.
Please, use as a VCS root only one of them.