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If we create a new top-level folder and link it to a Git repo, a private clone for the user is created on the server. This private clone will be shared by all top-level folders linked to the same repo. However if all top-level folders pointing at this private clone are deleted, the clone stays on the server. So far I would just delete it. When we provide the Git shell (Bug 336116), the user should have more control over it.
Clones created in the user area[1] are linked to projects in workspace. Removing a project doesn't remove a linked resource[2]. Not sure if there is anything we can do, without changing that policy. Added a test[3], ignored for now. [1] bug 338558 [2] org.eclipse.orion.internal.server.servlets.workspace.WorkspaceResourceHandler.removeProject(WebProject, String) [3] d0ba29457fff54cf34235a830b7fe15b74bf2a9c
*** This bug has been marked as a duplicate of bug 340553 ***