Two paths missed setting up overlays:
- `CompletionInstance` when checking files from dependencies
- `SwiftASTManager` when reading in files that it would later replace
all inputs with
(1) would cause the AST context not to be re-used, even though nothing
had changed. (2) caused all non-completion functionality to fail for any
symbols within files only specified by the overlay.
Resolves rdar://85508213.
