Separated UI refresh into 'style' and 'state' refresh to avoid race condition between task scheduler thread and UI thread that affected code view state.
fixes#916
* added "--shallow" command line option to request shallow indexing
* modified behavior of Sourcetrail to always perform a deep index if not explicitly specified differently by the user
* show proper error message in console when project configuration has issues
* quit when project configuration is wrong
* show indexing progress as self-updating percentage
* removed unused utilityMath
* removed some unused functions from utility
* moved time related utility functions to TimeStamp
* moved path objects from utility to app/paths
* moved objects in lib to lib/app
* removed duplicate confirm methods in DialogView
* moved utilityFile to utility/file
* removed uint typedef and replaced with size_t everywhere
* removed boost header in utilityUuid