As of Git 184.108.40.206 there is a special new feature for windows users. Thanks to Johan ‘t Hart, files and directories starting with a single dot (such as ‘.git’) will now be marked hidden (you can disable this setting with
core.hideDotFiles=false in your config) (Issue 288).
Which means if you have this version of git or newer when you checkout, all of the Eclipse project files will be marked as hidden on Windows. This makes them unwritable and causes problems.
[core] hideDotFiles = false
See this guide to make git repo information show in your shell prompt.
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