/usr/local/share/X11/ and /usr/local/share/etc/ are still directories, as Misalf mentioned best just to add individual files when possible, keeps backups small.
Control Panel -> BackupRestore -> Included For Backup -> most cases you would select Add File not Add Directory.
Example, etc/X11/xorg.conf, not the entire /X11 directory (bad example, probably just contains the one file).
Same with usr/local/share/etc/ (assume typo, don't think TC uses this directory).
You're saying Tor is configured in /usr/local? You would not backup the entire directory, just individual files required to maintain Tor persistence. Sorry not familiar with Tor's directory structure. Is Tor a *.tcz? If so then none of those files would require additional backup, unless you made specific changes or have additional configuration files not present in the *.tcz.
In TTY you can output to file. Example:
ls > /home/tc/list_of_files