Implement and document homebrew intake pipeline

[bgyss]

Summary

• expand docs and plans around exploratory pipeline, specs, and AGENTS guidance for the homebrew recompilation effort
• update the Rust pipeline/runtime crates plus samples, inputs, and tests to cover the new homebrew intake, module extraction, and runtime surfaces described in the specs
• refresh Cargo.lock and related configuration to keep the workspace consistent with the intake/runtime changes

Testing

• Not run (not requested)