For “cleaning up” things there’s the ]gc command in the Pkg REPL:
(jl_auRg37) pkg> ?gc
gc [-v|--verbose] [--all]
Free disk space by garbage collecting packages not used for a significant time.
The --all option will garbage collect all packages which can not be immediately
reached from any existing project. Use verbose mode for detailed output.
For a more thorough clean maybe look at:
I would encourage you to open a separate thread for plotting issues, which are unrelated to cleaning up Julia related directories - this is helpful for others who find these threads through searches later on.