Introduce more robust SBOL-based provenance

[marpaia]

Native SBOL3 components now supply design data to the experiment builders. Assembly, transformation, and plating preserve design identities in protocol samples and output manifests, and the examples save their designs graph alongside the compiled artifacts.

The focused LabOP follow-up is #14, stacked on this branch. Merge this PR first.

The compiler boundary is Protocol → compile(). Builders return a Protocol; the compiler no longer dispatches across experiment types. This removes Part, the three request wrappers, compiler overloads, and the compiler's inputs= argument. Assembly and transformation recipes refer directly to sbol3.Component objects, and provenance uses native SBOL3 types.

• Updates the cloning and transformation examples and adds a complete native SBOL provenance example.
• Covers saved SBOL designs flowing through assembly → transformation → plating, including identity preservation and isolation from later SBOL edits.
• Changes the public experiment API intentionally; the README and provenance guide show the new calls.

Review size against master: 1,186 changed lines (763 additions, 423 deletions), including tests, documentation, and the lockfile. Implementation code under src is reduced by 111 lines.

Local validation: 158 tests passed with robot SDKs, Ruff and mypy passed, all three examples ran, and fresh wheel/source-distribution installations passed the install checks. Remote CI is separate from these local results.