Having both rename-at and rename-all both seems confusing and introduces unneeded difficulties. Allowing to use both -qualified-name and -offset at once while performing efficient renamings seems like a feature, too. Maintaining main function wrappers and custom help becomes redundant while CLI becomes less confusing.
This is basically D23651 done right.
This patch belongs to a sequence of patches needed for painless migration to clang-refactor, see D24192.
No using declarations in headers, please. Also, since your code is in the clang namespace, you can include clang/Basic/LLVM.h that re-declares ArrayRef in namespace clang.