Looks like the biggest cuprit is repository/datastore.
crx-quickstart]$ sudo du --max-depth=2 -h .
202M ./launchpad/installer
4.7M ./launchpad/config
8.0K ./launchpad/conf
482M ./launchpad/felix
3.5M ./launchpad/startup
693M ./launchpad
2.3M ./repository/blobids
65M ./repository/index
12G ./repository/datastore
2.8G ./repository/segmentstore
15G ./repository
1.5M ./opt/helpers
1.6M ./opt/portal
76K ./opt/notsoserial
18M ./opt/filevault
33M ./opt/extensions
54M ./opt
3.8M ./threaddumps/20190604
1.2M ./threaddumps/20190606
4.0M ./threaddumps/20190605
3.9M ./threaddumps/20190405
352K ./threaddumps/20190602
3.0M ./threaddumps/20190531
400K ./threaddumps/20190406
168K ./threaddumps/20190525
2.8M ./threaddumps/20190603
20M ./threaddumps
12K ./monitoring
4.0K ./logs/ffmpeg
5.5M ./logs
40K ./bin
236K ./conf
463M ./app
16G .
I thought that's what the datastore garbage collection cleaned up...