I started using sourceTree I have a problem when I change certain files, I noticed those are files from my views folder (MVC), sourceTree marks it as:
Modified file,
Make sure that the config core.autocrlf
is set to false, to avoid automatic eol (end of lines) conversion on all your files.
git config --global core.autocrlf false
(and re-clone your repo to see if the issue persists)
See for more "SourceTree App says uncommitted changes even for newly-cloned repository - what could be wrong?"
This sourceTree thread points out also to .gitattributes
files.
The OP Asaf Maoz points to another source (in the comments), still related to eol:
the problem was in my IDE line endings settings, some files line endings was set to MAC (when I am not on MAC) and ST could not convert them properly.