I recently ran across the following issue:

I backup my workspace on a regular basis using the built in backup/zip tool.
I used the tool to turn my library into a filesystem directory.

When I went to restore my project after some issues, I realized that the backup tool was NOT backing up the filesystem directories. So my code and reports were NOT being backed up.

Luckily I had a manual backup of my whole system otherwise I would have been toast.

Has anybody else run across this? I know you can add extra files to the backup, but that would require you to remember to update those selected files in the backup system every time I added some code or a report.