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Hi H Shah,
I pushed some changes to my local branch and updated the tests cases:
https://github.com/charleswhchan/patch-parameter-plugin/tree/JENKINS-27169/src/test/resources/org/jenkinsci/plugins/patch
Specifically, I created 2 patch files. One file for UNIX platform (LF line ending) and the other for Windows (CRLF line ending).
Then each patch is applied against foo.txt and verifies the output ends up in the native line ending format.
https://github.com/charleswhchan/patch-parameter-plugin/blob/JENKINS-27169/src/test/java/org/jenkinsci/plugins/patch/SomeTest.java
So base on the tests, your scenario should work?
Feel free to run and modify the test and let me know of your result.