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I've been noticing this for a while now and don't know why it happens.
When staging a hunk and hit commit, it commits instead the whole file and not just the hunk I staged.
This happens only with some repos, in some others it seems that it's working like it should, that is committing only the staged hunks/files.
I've not experienced that behaviour. Is it reproducible on demand?
Which version of Sourcetree are you running? And can you add some more detail about the order of events, which buttons where you are clicking etc?