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Work-around: You are free to open a second window, e.g. by double-clicking a different repository.

What exactly do you mean? Please describe more detailed what you expect.

Do you know the "Recyclable Commits" option in the Log's Branches view?

If I don't forget, I will update the documentation on how to modify the theme using a properties file. This will also allow to modify the toolbar's background color.

Not everything is possible to change. The toolbar foreground color can't be changed at the moment on Windows (see SWT bug above) - hence I rather keep it as is. The tree triangles can't be changed, too, the table headers and scrollbars, too. The Changes view coloring you can change in the preferences. It is configurable by the user and hence not affected by the theme.

This feature works already fine. If you really have 2 or more processes of SmartGit hanging around, please conttact the support (see Help menu).

SmartGit already should connect to already running instance. If not, I consider it a bug.

Local | Toggle 'Assume-Unchanged' is your friend.