I guess that answers my note from earlier, ha.
I uploaded a new version that adds an option to Project Properties.
There's an improvement but there are still two related problems:
1) It seems the .yy files are still doing Windows line endings, even if you tell it to use Unix line endings
2) The ///@desc are being changed to use Windows line endings too (probably being re-written by the editor?)
I know this because if I open the touched files in sublime, and enforce again to Unix line endings, the differences in sourcetree disappear.