Fix modules codegen to be compatible with modules-ts

The Module::WithCodegen flag was only being set when the module was
parsed from a ModuleMap. Instead set it late, in the ASTWriter to match
the layer where the MODULAR_CODEGEN_DECLs list is determined (the
WithCodegen flag essentially means "are this module's decls in
MODULAR_CODEGEN_DECLs").

When simultaneous emission of AST file and modular object is implemented
this may need to change - the Module::WithCodegen flag will need to be
set earlier, and ideally the MODULAR_CODEGEN_DECLs gathering will
consult this flag (that's not possible right now since Decls destined
for an AST File don't have a Module - only if they're /read/ from a
Module is that true - I expect that would need to change as well).

llvm-svn: 293692