[PM] Make the AnalysisManager parameter to run methods a reference.

This was originally a pointer to support pass managers which didn't use
AnalysisManagers. However, that doesn't realistically come up much and
the complexity of supporting it doesn't really make sense.

In fact, *many* parts of the pass manager were just assuming the pointer
was never null already. This at least makes it much more explicit and
clear.

llvm-svn: 263219