[opt] Fix run-twice option for non-idempotent passes

[opt] Fix run-twice option for non-idempotent passes

Cloning the module was supposed to guard against the possibility
that the passes may be non-idempotent. However, for some reason
I decided to put that AFTER the passes had already run on the
module, defeating the point entirely. Fix that by moving up the
CloneModule as is done in llc.

git-svn-id: https://llvm.org/svn/llvm-project/llvm/trunk@254819 91177308-0d34-0410-b5e6-96231b3b80d8