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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
With SmartGit 17.1 preview 3 it becomes easier to create own themes: http://www.syntevo.com/blog/?p=4391.