What To Do in an Emergency
If you get your Dakota project in a tangled mess and are afraid to lose any work you may have done, do something like the following for any repository you have work to salvage (eg core Dakota, pecos, local):
Checkout a new local emergency branch, e.g.
git checkout -b imstuck
Add any new files unknown to git, e.g.
git add new_file1.hpp new_file1.cpp new_file_readme
Commit everything, e.g.
git commit -am "Capturing WIP and getting help"
Walk away slowly
Contact the Dakota infrastructure team, or another Git guru.