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Save open repositories without closing the application
In Ubuntu it is necessary to close the application so that the open repositories are kept in the sidebar

Handle invalid special characters for Windows
If you pull from a repo containing a file such as Invalid<"file">.xml then SmartGit on Windows throws error messages about not being able to stash, merge, etc. The only route forward issuing gitbash to resolve before you can resume using SmartGit.

Custom ordering of groups and repositories
Alphabetical ordering doesn't really scale well when you work with a lot of repositories. I'd like to be able to custom order (either via drag-and-drop or arrow buttons) my groups and repositories so I can shift them around as priorities change without needing to put them in "A Most Important Group!"

"Finish feature" in git flow should push dev branch
Some git flow operations (hotfix finish, release finish) push master and dev branches to origin, but Finish feature does not. I found myself self several time having not pushed dev branch as I expected Finish feature will do all steps required.

Journal: option to hide common commits [SG-10558]
If i had one commit unpushed i wanted to see it down below in the outgoing section. The problem here is that there is no option here to filter only the unpushed items.

Diff tool should insert code difference, for example, when SHIFT key is pressed
Right now when you compare changes in two panel diff tool, or three panel diff tool you can got case when diff tool allows you only to replace code. It can happen when in two branches the same line of code has been changed and you are trying to merge these files.
It would be great to have possibility to force diff tool to insert diff line if SHIFT key is pressed.

When receiving the message "the following untracked working tree files...", allow the user a choice.
When switching to/from a branch where new files are added sometimes files are left behind (soapui project xml for example), when switching back to the branch with the new files you'll often get the warning "The following untracked working tree files would be overwritten by checkout", and a list.
It would be nice to have an option added to this dialog to basically say "ok, overwrite them". Instead of having to look them up 1 by 1, and manually deleting them before trying to switch to the branch a second time.

Ours and Theirs are confusing, add more info everywhere it's used in GUI
Everytime I have a conflict in git and I need to resolve it by choosing "Take Ours" or "Take Theirs" - I get confused
I roughly remember that if I do merge - Ours is mine, Theirs is remote
If it's rebase - it's reverse... when applying stash - it's something else...
So thinking about this is hard.. and I am never sure I got it correctly
What I do in the end - I right click file, go to commit log... look at commits and then select file and "Save as after" and Stage to resolve the conflict so I really know which commit is "ours" and which commit is "theirs"
My suggestion is:
everywhere where in UI you write "Take Ours" and "Take Theirs" - do add more info i.e.
Take Ours (<hash> <branch> <author> <message>)
Take Theirs (<hash> <branch> <author> <message>)
It's especially helpful with non tech people (like artists)
Explaining to them insanity about "ours" and "theirs" is pretty much impossible
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