If your phone uses the sdcard for primary storage, then you can mount your phone on your computer without removing the card and use rsync from the command terminal on your computer, at least until you get the app sorted out.
/media/FC30-3DA9 was the mount point and /opt/Android_rsync was the target folder. File permissions on everything should be retained, but you'll have to verify the mount point and be sure that the target folder is R/W. I can't do this anymore because the N4 uses MTP, but it worked really well for my old phone and made regular backups very fast and easy. The Android app might be a better solution, however I just never tried it.
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