Just in case: I see you seem to be battling against CRLF For instance: https://github.com/apache/maven-checkstyle-plugin/pull/16 Did you consider to add the relevant .gitattributes file to ensure Git converts the files automatically? With a proper .gitattributes file, it is just impossible to commit a file with "a wrong EOL".
PS. I've came across this thread when Apache JMeter project noticed that Window-based builds were broken by https://issues.apache.org/jira/browse/INFRA-18383 Vladimir
