possibly missing `by_alias=True` for freeze format models

we're expecting things like "basic blocks" in the freeze format, but we're missing `by_alias=True` in the Pedantic models, so I don't think they're being generated as documented/expected.

Start by locating the Pydantic models involved in freeze format generation and the code that serializes them. Check whether alias-based serialization produces the documented "basic blocks" entries, then verify the generated freeze format against the expected structure.

Written by the indexing model from the issue text.