Please post output of "git config -l | grep core" invoked in your Windows and your Linux repository.

So you have separate clones on Windows and Linux? Then Git's default line endings handling should do exactly what you want.

There are a couple of additional things happening during a Refresh, compared to a "git status". Either way, please send periodical thread dumps for a subsequent refresh to smartgit@syntevo.com : http://www.syntevo.com/doc/display/SG/Periodical+Thread+Dumps

Right, that's what this RFE is for.

The GUI is actually not expected to change.

That's true. The option will just execute the system Git-Flow command instead of SmartGit's built-in Git-Flow. So your request makes perfect sense.

In the Preferences, section Executables, you can select Use pre-installed ("system") Git-Flow.

Sounds like a generalization of topic http://smartgit.userecho.com/topics/419. We most likely won't implement concurrent Git operations, because of all the possible problems when accessing a complex database (like Git) concurrently.

This sounds like a bug. Does "git status" show proper results?