On Windows, you could move the configs elsewhere, make a symlink to them in the old place, and mark the symlink as hidden so you don't see it in explorer. Too bad this can't work on Linux because the hidden-state is encoded in the filename.
Well, the hidden-bit on Windows is really semantically equivalent to dot-prefix on Unix, and people set up their file managers to show such files for similar reasons (I don't even use Explorer, mostly). In Win10, it's even exposed as a setting in Settings | For Developers
For actual file management, and generally working in the terminal, I'm firmly in the "two blue panes" club, so it's Far Manager on Windows (and Midnight Commander on Linux). Far is probably the most advanced text-mode file manager in general right now.
Compared to 15 years ago I think Explorer is much better now, it could be even called usable.
Nevertheless there are alternatives. One liked by many are Norton Commander alike file managers like Total Commander or even Far. I am not too much in favor of them though.
I like to use Directory Opus. It is powerful and flexible. Costs money though.
