QbsProjectManager: Fix overriding of properties.

We have to mark the user-set properties appropriately; otherwise,
properties in project files will not get overridden.

Change-Id: I3bcb013fde2b76521a85c3283e2b158beaf40b26
Reviewed-by: Joerg Bornemann <joerg.bornemann@digia.com>
Reviewed-by: Tobias Hunger <tobias.hunger@digia.com>