* Root folder variable names are now more descriptive
* clone_repo() now restores the current working directory
* Removed setup_upstream_repo() since it's now identical to clone_repo()
* Moved am_patches()'s for loop into user scripts so the filename prefix
doesn't need to be included in every patch filename
* Renamed am_patches() to git_am() since its only job now is to run "git am"
* Removed unused apply_patches() function
* Fixed typo in git_am()'s ignore_whitespace arg name
The template argument order for UnscentedTransform was reversed to match
all the other UKF classes. Since UnscentedTransform is intended as a
class for internal use only, this shouldn't cause much breakage.
