[clang-tidy] Fix run-clang-tidy.py.

Do not add "-*" to the list of checks. Make consistent the list of enabled
checks and the checks in use. Moreover, removing "-*" makes the behaviour
consistent with clang-tidy and allows user to use .clang-tidy configuration...

http://reviews.llvm.org/D12687

Patch by Marek Kurdej!

llvm-svn: 247002