[SBS-CONNECT-EPIC-02] Make the clean BuildCompiler API integration-ready

[Gonza10V]

Notion task: https://app.notion.com/p/39f1a3339dcb812b9ac6cbe203f456a2

Objective

Complete the clean token-based SynBioHub factory, JSON-safe result boundary, SBOL validation gate, and immutable release required by SynBioSuite.

Program

• Notion hub: https://app.notion.com/p/39f1a3339dcb818ea29eec44007d8e6e
• Release: R2 Planning Preview
• Type: coordination epic — do not send this parent issue directly to Codex.

Shared constraints

• Do not integrate through the legacy BuildCompiler class.
• Do not add email/password handling to BuildCompiler.
• Keep PUDU and Opentrons optional.
• Build on existing refactor issues [EPIC-01] Domain contracts, options, and API foundation for full_build refactor #52–[ISSUE-15] Add end-to-end fixtures and modernize core CI #67 and [SPRINT-02] Indexing, SBOL artifact, and protocol boundary stabilization #87–[SPRINT-02-12] Validate plating/protocol JSON boundary and optional simulation behavior #99 instead of duplicating them.

Child issues

Child checklist will be added after feature issues are created.

Success criteria

• All child issues are complete and verified.
• Cross-repository dependencies are reconciled.
• Required security/biological human checkpoints are complete.
• Notion task states and GitHub issue states agree.

Rollout

Implement child issues as focused pull requests in dependency order.