Fix resolver stdin handling for --with dependencies

[t-kalinowski]

Summary

• Read resolver input from file("stdin") so ir run --with ... reaches the embedded R resolver through Rscript’s real stdin stream.
• Add a CLI regression that exercises the public ir run path against the real R resolver and verifies a --with package is materialized into the runtime library.
• This fixes the case where dependency specs were being skipped by the resolver, leaving the dynamic package library empty for user code.

Notes

• The change is internal-only in the resolver path; the user-facing behavior is that --with packages now resolve and load as expected.