Fix breakage of some compile_commands.json users

Depending on the user, the PrepareClangFlags rewrite of a few commits ago could
break users with an extra "clang: 'linker' input not used" (or similar) error
message because the compiler executable string was not removed from flags
upstream if the user prepended some flags to the output of PrepareClangFlags
before returning it to the caller of FlagsForFile.

Since the rewrite was supposed to be backwards compatible, this needs
to be handled.