Great question — answering as the UphillTech team:
The two symptoms you listed: ls takes a long time. Directory-removal takes a long time. both point at the storage (also known as "disk") and/or filesystem problem(s). You'd need to research, how to speed these things up to match your needs. Further, your top -snapshot shows Subversion running -- and busy in the biowr -state, which points at the same. Subversion can be quite heavy on the storage -- if you try other operations exercising the same storage-device Subversion is currently updating, you may be slowed down just by that. The good news is, only the I/O is delayed -- the rest of your system is idle and could, for example, be used to play a movie, compile something, or, indeed, manage...
Full answer by Mikhail T.: https://superuser.stackexchange.com/a/1818422 (CC BY-SA 4.0).
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