Removing this mechanism is beneficial since the mechanism relied on
USES INCLUDE headers which were used in inner loops and contained
CCTK_IsThornActive call which would execute in each inner loop iteration (see meeting minutes http://lists.einsteintoolkit.org/pipermail/users/2013-December/003343.html for 2013-12-02).
Pull request https://bitbucket.org/einsteintoolkit/einsteinbase/pull-requests/2/tmunubase-remove-deprecated-support-for finally removes it
Associated pull requests to handle thorns that used this functionality (Exact) and would not show up in Tmunu anymore are in comments below.