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Once bug 336116 we should remove GitFileStore, since we all agreed that auto-commit/auto-push approach is wrong. In the meantime, we could at least remove the gitfs option while linking a project and mark the file store as deprecated pointing to the git REST API (bug 336116). Fixing bug 336116 would also greatly improve the issue described in bug 334094.
org.eclipse.orion.server.filesystem.git, server.sshconfig.home, server.sshconfig.userprofile and server.tests.filesystem are no longer referenced by any Orion server plug-in or feature. I left them in the repo though in case we need to reuse the code. I also raised a bug for releng to remove all references to these bundles, see Bug 339868.