Reclaiming occupied space A MBPro with a 250GB running the latest Mojave suddenly went from 100GB+ of free space to 5GB and is warning us about running out. Looking at About>Storage>Manage, it seems most of the occupied space is System (168GB worth). Looking at things via the Finder, we only see about 90GB of stuff total and only 9GB in the System directory and 6GB in the main Library folder.  Running OmniDiskSweeper with the sudo command via Terminal, it confirms what the Finder is reporting…that there should be about 90GB instead of 245GB of stuff.  We also ran GrandPerspective and it does not “see” any inordinately large files.

Researching a bit, I found some possibilities that haven’t panned out.
1. it’s NOT local TimeMachine snapshots, as was the answer for some people
2. it’s NOT a runaway Spotlight index, as it was for some people
3. running TimeMachine did NOT clean things up, as reported by some
4. revealing hidden files did NOT reveal anything out of the ordinary
5. booting into Recovery Mode and running Disk Repair reported everything fine

Some have thrown their hands up wiped out their hard drive and reinstalled (which has fixed this issue for some).
 The problem is, my friend with this laptop is traveling thru Europe and is not technically savvy. So, talking her through a full reinstall will be a big challenge.

There must be SOME way to see what’s occupying the space.   It would seem to me that perhaps there’s some that went wrong with the recent conversion from HFS+ to APFS when she installed Mojave. 

Any ideas on how to reclaim the space without reinstalling from scratch?
Turns out the answer came out of left field. I had done a Spotlight rebuild, which didn't reclaim the space, but what it did do (I think) is change totals in About>Storage>Manage. The System went down to 90GB (which is still high but better), but Mail jumped up to 95GB. That gave me the clue to look in the ~/Library/Mail folder. From here it gets weird.

Turning on 'Calculate folder sizes' in the Finder, it calculated the Mail folder as 24GB.  However, underneath that folder were several "mail container" folders, one of which was 37GB besides another that was actually 24GB. Literally it didn't add up.

Inside of that 37GB folder was a Drafts mbox was 37GB all by itself!  

Over in Apple Mail, she had no visible Drafts folders in any of the three accounts. I checked preferences to make sure each account was pointing to a server Drafts folder, and they were.  And when I created a new draft, it showed up properly.  So, the functionality was fine.

So, I figured out which Gmail account this huge Drafts folder belonged to (by watching the timestamps on the folders when I updated in Apple Mail), and then logged into that Gmail account via web. There I found a Drafts folder with hundreds and hundreds of emails with attachments (its normal for her to work with large PDFs).  These Drafts weren't getting deleting when she sent them.  So, I cleared all the Drafts off the server.  However, when I later launch Mail, the "cleanup" I was expecting didn't happen. Somehow, the Drafts mbox was a separate copy of these abandoned Drafts.

So I was left with quitting Apple Mail and Finder-trashing the 37GB Drafts mbox.  Even though the ~/Libary/Mail folder didn't gain any space, the overall hard drive free space did (as well as About>Storage>Manage).

She's got enough free space to work with now, but System still shows as 90GB and we don't know how she got into this predicament in the first place.  So, we don't know if this is the end of the saga.  (Perhaps because she travels a lot, she's "offline" a lot and Gmail is being ultra conservative saving her Drafts?) I suppose when she's back from her travels, I'll zap that email account and re-enter it, so it can download a fresh copy from the server.