And once you've cleared the extra cruft from your .kobo directory, you'll want to read the NOTE I added to the first post so that Nickel won't try to index stuff from inside KOReader & Plato's folders, even when they're installed in the right place

.
(And probably you'll then have to reinstall 'em, because Nickel will have deleted a few icons in the process ^^).
TL;DR: Don't get it wrong on FW 4.17+, or things get slightly trickier. Or just use the install scripts, they take care of everything.