VcsManager: Fix soft assertion when directory is managed by 2 VCS

In case 2 VCS manage the same directory, topLevel will be the same
for both. Chopping tmpDir gives a wrong directory for the second VC.

Change-Id: Ie20c716cf8b713dae0d5d8ecc4c947f1c5029544
Reviewed-by: Knut Petter Svendsen <knutpett@pvv.org>
Reviewed-by: Tobias Hunger <tobias.hunger@digia.com>