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Eclipse on Linux writes launch configurations with Unix line endings, ignoring project specific and workspace line delimiter settings. For shared launch configurations under version control, this leads to conflicts. This is particularly problematic if launch configs are configured with an "Alternate JRE": Renaming the JRE in the workspace settings will cause every single launch config in the workspace to be modified. For us this means hundreds of files in dozens of projects. Reverting those modifications without reverting the real changes is very time consuming. And accidental commits lead to confusion, because developers don't understand why the files changed and the diff doesn't show any changes (if whitespace is ignored). Playing with the settings on the JRE tab in the launch config dialog will also cause the file to be modified. The best solution would be for Eclipse to keep the existing line delimiters in existing launch configs. Second best option would be to honor the project specific settings for new file line delimiters (although these are not "new" files). Third best option would be to honor the workspace settings for new file line delimiters (although these are not "new" files).
Also see: https://github.com/eclipse-platform/eclipse.platform.debug/issues/29