Note when a decl is used in AST files.

When an AST file is built based on another AST file, it can use a decl from
the fist file, and therefore mark the "isUsed" bit.  We need to note this in
the AST file so that the bit is set correctly when the second AST file is
loaded.

This patch introduces the distinction between setIsUsed() and markUsed() so
that we don't call into the ASTMutationListener callback when it wouldn't
be appropriate.

Fixes PR16635.

llvm-svn: 190016