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I've been working on a Minecraft Forge Project and when I get Egit to work with it. It attempts to delete all my project files from the repo. Afterward it ignores all changes to the files--kindof. It tracks a change to a class file, when the src files were not built between commits. The project is a git repo inside an eclipse project.
I don't understand your problem report. Can you provide a minimal sample project and steps to reproduce ? Also can you specify which EGit/Eclipse version you are using ?
Before I make any changes to the files (git shows no changes) Egit says I have unstaged changes. I staged these changes and Egit deleted the file from the repo. https://github.com/BinaryAura/Stamina is my current Repo. Follow the README.md instructions to reproduce. I have Eclipse Mars (4.5.0) and EGit v4.0.0.201506090130-r