[BC-INTEGRATION-03] Resolve authenticated tutorial SBOL validation failure

[Gonza10V]

Notion task: https://app.notion.com/p/39f1a3339dcb8130a49ed21172a16d9d
Parent epic: #111
Notion program: https://app.notion.com/p/39f1a3339dcb818ea29eec44007d8e6e
Temporary ID: BC-03
Release: R2 Planning Preview
Dependencies: BC-01, BC-02, BuildCompiler #97, #98
Codex-ready: yes after dependencies are satisfied

Goal

Turn the SBOL validation failure recorded in the authenticated tutorial into a reproducible fixture and make generated build documents pass the agreed validation gate.

Expected files/modules

• notebooks/buildcompiler_synbiohub_authenticated_tutorial.ipynb
• src/buildcompiler/sbol/
• tests/integration/

Scope

• Extract a minimal offline fixture reproducing the String-to-URI validation problem.
• Fix serialization/provenance construction at the correct SBOL boundary.
• Validate serialize/reload plus the supported validator.
• Document any upstream pySBOL2 validator limitation explicitly.

Non-goals

• Do not hide validation failures.
• Do not broadly rewrite assembly biology.
• Do not require live credentials in core CI.

Acceptance criteria

• The previous failure is reproduced by a test before the fix.
• Generated build document serializes, reloads, and passes the agreed validation command.
• The notebook no longer contains a contradictory failing output.
• Human SBOL review is recorded.

Verification

• Run focused SBOL tests and full core suite.
• Execute notebook-equivalent workflow with offline fixture.

Risks and review

• Risk tags: SBOL-validation, biological-semantics
• Human checkpoint required: yes
• Treat AI-generated changes as unreviewed until tests and human review pass.

Codex handoff

Implement as one focused PR. Begin by verifying dependencies and current repository state. Preserve unrelated work. Report implemented behavior, tests, commands, assumptions, and blockers.