Gabriel,
Unfortunately this seems to be a bug with the Subclipse plugin, this came back from one of our devs:
The issue is that the subversion plugin is not properly marking its
resources and directories using IResource#setTeamPrivateMember, which
instructs the rest of the workbench, including our deployers, to ignore the
resource. Since the subversion plugin is not setting this properly, it’s
impossible for the deployer to tell if the directory is part of the
application or not. Since the CVS plugin sets this as required, we ignore
CVS directories