This fixes two issues:
1. The SwiftPM build system was setup without passing through whether it
should prepare or not. This meant that we lost eg. the argument to
allow compiler errors when building the AST (even though it was set
when building the modules)
2. The compiler argument adjustment to remove harmful and unnecessary
flags only applied to indexing arguments, not those passed to the AST
builds
Resolves rdar://141508656.
