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What is "Clean" files and how to stage them?

Edited

We can show files with status "Clean" in the Sourcetree. I also have several (a lot of) these files in my project. One part of these files is also ignored (because of they are in .gitignore), but another looks like normal files. There are on my disk, but not in repository and I can't commit them to my repo. If I press "Stage" or press "Untrack" then "Track" again it doesn't work. They are still in "Clean" status in unstage section. How to solve this issue?

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