I've used Forklift for years, very stable: http://www.binarynights.com/forklift/

Actually, Forklift is broken in El Capitan, at least for me. It just freezes after few seconds upon launching and then fails to recognize user input, or lags terribly.

I would do, but it fails to open my OpenLDAP/nfs mounted home :(

On Windows I've been using Total Commander for 15 years or more. There's nothing like it on Mac, and I've tried them all. But there's this new app, Files (http://filesmanager.info/), which is being actively developed and gaining features fast. I've been using it for some time now I'm liking it more and more. The developer behind it is very responsive and skilled and it seems to be going in a great direction. There's hope for OS X! :)

Thanks, the free lite version is definitely enough for me! (although there may be other unexpected ways to generated the .DS_Store files)

But finally I just use clean.sh when necessary. :P

For source code repos, yeah. Otherwise, add .DS_Store to your .gitignore.

Cocoa tech Path Finder for me.

I second the Path Finder recommendation:

http://www.cocoatech.com/pathfinder/