If your project has too many directories and/or files it may cause the file system scanners to fail, you may want to increase the maximum execution time of the PHP scripts and the memory limit to allow the functions executed during the file system scans to finish successfully. If you do not want or do not have sufficient privileges to increase these values then you may want to skip some directories, this will force the plugin to ignore the files inside these folders.
The feature to ignore directories during the file system scans is disabled, go to the Scanner Settings panel to enable it.