Use dependecies for residual UO computation
closes #3984
Switch pc over to shared pointers
Convert Predictor to shared pointer
Convert Timestepper to shared pointer
Convert functions to shared pointers
Convert ICs to smart pointers
Switch Indicators over to shared pointers
Convert markers to shared pointers
refs #3692
Fix logic/clean up repo version script
closes #3998
Merge pull request #3999 from permcody/warehouse

Warehouse
Merge pull request #4000 from permcody/repo_ver_fix

Fix logic/clean up repo version script
Merge pull request #3995 from idaholab/dont_compute_aux

Use dependecies for residual UO computation
Merge commit '412e1d9c6674d0a7e18e37167976184ebe28c275'