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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.
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