Non bootable Mac Book Pro - What directories to salvage

My wife's 2012 13 in macbook pro stopped working after an update.  I tried everything I found in the forums to reinstall the OS, repair the drive, and to get it working again all with no luck.  As a last resort I ordered a Thunderbolt to Thunderbolt cable and was able to get the HD to show up in Target disk mode.  I copied the users directory and was able to save that to an external drive.
My question is if I want to rebuild this mac after we get it working again, what other directories do I need to salvage while I can?

All User-specific files (including System Settings) are in The Users directory.
The only other things NOT re-Installed with Mac OS X are any special Applications you installed, but you are better off installing those from their original sources than working hard to copy possibly damaged ones from a questionable drive.

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