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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.
Does Eclipse documentation automatically occurs like a tooltip or is it triggered by a shortcut as in IDEA?
Customer support service by UserEcho
We've added a tiny blue information icon in the top right corner of the commit dialog. Please move the mouse over it.