[PCH] Fix reading from PCH of diagnostic pragmas.

In certain cases ASTReader would call the normal DiagnosticsEngine API to initialize
the state of diagnostic pragmas but DiagnosticsEngine would try to compare source locations
leading to crash because the main FileID was not yet initialized.

Yet another case of the ASTReader trying to use the normal APIs and inadvertently breaking
invariants. Fix this by having the ASTReader set up the internal state directly.

llvm-svn: 144153