[SPRINT-02-12] Validate plating/protocol JSON boundary and optional simulation behavior

[Gonza10V]

Parent sprint: #87
Depends on: #93, #94, #97, #98
Recommended order: 12
Codex-ready: yes

Goal

Validate the current plating/protocol boundary honestly: plating is currently metadata/file/protocol-output oriented, not a full SBOL-object stage. Add tests and small fixes so JSON/CSV/manual outputs are deterministic and optional simulation behavior stays optional.

Background

BuildCompiler.plating() currently normalizes transformation output, assigns 96-well positions, writes plate-map JSON/CSV plus a layout CSV, and can write either a manual Markdown protocol or an automated protocol script. The method explicitly does not create new SBOL objects for plating. robotutils.normalize_plating_input(...) is the key boundary between transformation output and plating artifacts.

This sprint should validate the existing boundary before adding any future plating SBOL feature.

Scope

Add tests for:

• normalize_plating_input(...) consuming transformation output from [SPRINT-02-11] Harden transformation SBOL output and chaining tests #98;
• deterministic well assignment for one or more transformed strains;
• plate-map JSON shape;
• plate-map CSV shape;
• manual protocol Markdown creation;
• automated protocol script creation without running simulation by default;
• simulation errors being reported/skipped safely when optional tools are unavailable.

Small fixes are allowed to make output deterministic, safer, and easier to test.

Non-goals

• Do not make plating a full SBOL stage in this issue.
• Do not require Opentrons or PUDU in core tests.
• Do not run hardware/simulation tools by default.
• Do not add wet-lab instructions beyond existing high-level manual protocol metadata.

Acceptance criteria

• Plating consumes transformation output from [SPRINT-02-11] Harden transformation SBOL output and chaining tests #98.
• Well assignment is deterministic and tested.
• JSON and CSV outputs are written only to explicit temporary/output paths in tests.
• Manual protocol artifact is produced in manual mode.
• Automated script artifact is produced in automated mode without requiring simulation success.
• Optional simulation remains optional and failures are captured in logs rather than breaking core compiler-only workflows.
• Core tests do not require PUDU or Opentrons.

Verification

pytest -k "plating or protocol or normalize_plating_input"
pytest -m "not automation"
ruff check .

Codex implementation notes

• Use tmp_path for all file-writing tests.
• Do not write files into the repository root.
• Keep this issue focused on current behavior and testability.
• If future plating SBOL support is needed, open a follow-up issue instead of mixing it into this one.