Git pull not correctly solving conflicts on the absence of conflicts

[PgBiel]

Description

Sometimes the web app is trying to be too smart when doing a pull on git integration. I can make some changes, but then undo the changes to avoid conflicts when pulling - say, by pasting the old version of the file (in the latest commit previously pulled by the web app) on top of the modified version to get fully rid of my "dirty tree" state in the web app -, but if I do that, that seems to consistently cause problems when pulling. The file gets apparently scrambled, with changes appearing together at the top, or with some changes being skipped (lines that should have been deleted but weren't, for example).

Reproduction URL

No response

Browsers

Firefox

OS

Linux