Your comments
Currently, this opens a dialog where you can select the file to compare with (the file might have been moved or renamed in the mean-time). Should we really open this dialog for each selected file?
We've added a tiny blue information icon in the top right corner of the commit dialog. Please move the mouse over it.
You may try following in SmartGit:
- show files recursively
- remove all tracked files but keep them physically available
- commit them
- add all "untracked" files
- amend-commit them
Now the latest commit should only contain files that were considered ignored. Alternatively, you may create a tiny script that invokes your above mentioned commands and add that to the Tools section in the preferences.
You already can share tools.xml.
Feel free to give it a try at SmartGit 18.1 preview.
Here comes a first glimpse of the new coloring mode. We plan to release a preview build the next week.

Ctrl+click is a bad choice because it is used in a tree-control like the Branches view to toggle selection. I know that in some text editors it is used to open links, but a text editor is something different than a tree control.
Please try the context menu of the "Commits" view, not the "Files" view.
Customer support service by UserEcho
Compare Before and Compare After depends on what compare you want to trigger - think about some reverted code or a commit from a different branch.
So I understand that you don't care about being able to edit the local path.