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Line endings and encodings are a known pain (and I am not fond of CM tools that 'improve' content). Suggest: EGIT request confirmation if text files are committed with inconsistent staged/indexed usage. In addition to OK/Cancel, the confirmation could offer additional tools prior to commit. a) change project(s) line endings preference - Linux encouraged b) change project(s) encodings preference - UTF-8 encouraged c) convert project files line endings d) convert committed files line endings If the staged/indexed files are a mess, just offer a report of the mess (unless you feel like offering a more substantial clean-up-the-mess wizard). i.e. you offer a more predictable auto-crlf functionality as an interactive tool rather than depending on users understanding the very hard to comprehend auto-crlf options.