I go into more detail in JENKINS-41177, but when I do job updates with the remote API line endings are changed. Two versions that were both edited in the UI or both by remote update will compare fine, but when mixed the line endings marks the entire files as different. I use a fork of the same diff-utils-lib (bkromhout:2.1.1) for a local diff before submitting the update and have the same issue there. By enforcing the same line endings (or just removing them when tokenizing into lines) I can get just the content differences.

This wouldn't fix the other two problems i have in JENKINS-41177 but would eliminate most of the false differences shown in the UI.