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Editing .gitignore outside workspace is not refreshed with F5. Use of F5 on a project does not re-check the .gitignore files have not been added/delete/modified. Furthermore to this even if I use "Team -> Ignore" to make Eclipse create a .gitignore and then replace the file with new contents (from outside of Eclipse), then press F5. I unset Project Explorer -> Filter -> .* resources, so the .gitignore is visible. If I open the file, it still displays the old contents (like Eclipse has cached the data contents). So this bug is about use of F5 to make EGit refresh its view of .gitignore files. I would expect it to pickup new contents.
Files outside a workspace are not resources and therefore not recognized as changed. Fortunately you can now create a super project at the top of the repository, thereby making all files resources which solves the issue. If you ignore .* resources, you still need to use F5. Maybe that's a platform bug, rather than a feature since .* files are usually essential to the proper operation of Eclipse.