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Do I understand you correctly, that you want to add the same repository (= directory) to different repository groups? That won't be possible because we maintain a set of directories.
With SmartGit 17.1 preview 3 it becomes easier to create own themes: http://www.syntevo.com/blog/?p=4391.
Currently following option can be used to customize the cherry-pick-message: http://www.syntevo.com/doc/display/SG/System+Properties#SystemProperties-smartgit.cherryPick.shaPrefixproperties.smartgit.cherryPick.shaPrefix
Please distinguish between 2 windows and 2 instances. If 2 instances of SmartGit are running (with the same settings directory), this is a bug. But 2 or more windows is by-design.
Because the log already shows the stash commits, this request seems covered by http://smartgit.userecho.com/topics/27 and http://smartgit.userecho.com/topics/28.
Do you mean independent repositories or submodule repositories inside one outer repository?
Implemented because now it can operate on the selected files.
Customer support service by UserEcho
Just select both commits (where the branches point to) in the Log and you will see the diff in the Files view.