[SPRINT-02-01] Add local SBOL document indexing entry point

[Gonza10V]

Parent sprint: #87
Depends on: none
Recommended order: 1
Codex-ready: yes

Goal

Add a first-class local SBOL indexing entry point so BuildCompiler can index already-loaded sbol2.Document objects without requiring SynBioHub registry credentials, auth token, or network access.

Background

The current BuildCompiler.__init__ takes collections, sbh_registry, auth_token, and sbol_doc, creates a sbol2.PartShop, and immediately calls _index_collections(collections). _index_collections treats every collection item as a URI and calls self.sbh.pull(uri, self.sbol_doc). This makes local/offline SBOL collection debugging difficult and hides whether a collection was actually indexed from local data.

Scope

Implement one of these equivalent APIs, choosing the smallest compatible change:

BuildCompiler.from_local_documents(
    collection_docs: list[sbol2.Document],
    design_doc: sbol2.Document | None = None,
)

or:

compiler = BuildCompiler(... minimal args ...)
compiler.index_document(collection_doc)

Preferred direction:

• Keep existing constructor behavior working if tests or notebooks rely on it.
• Add a new factory/classmethod for local documents rather than breaking current users.
• Reuse the same indexing logic that SynBioHub-pulled documents will use in later issues.
• Avoid any SynBioHub calls in local mode.

Non-goals

• Do not implement a full clean-architecture rewrite.
• Do not implement new route selection, assembly, or protocol behavior.
• Do not require PUDU, Opentrons, or SBOLInventory.

Acceptance criteria

• Local sbol2.Document objects can be indexed without constructing a real sbol2.PartShop or calling pull.
• The local entry point populates the same runtime state used today: indexed_plasmids, indexed_backbones, restriction_enzyme_implementations, and ligase_implementations.
• The local entry point can accept at least one collection document and a design/main document.
• Existing constructor behavior is not broken.
• At least one smoke test proves local indexing uses no network or SynBioHub pull.

Verification

Run:

pytest tests/unit tests/integration -k "local and index"
ruff check .

Adjust test paths if the repository currently uses a different layout.

Codex implementation notes

• This is a seam-creation issue. Keep it minimal.
• If the current constructor is too rigid, add a private alternate constructor/helper rather than rewriting the class.
• Prefer explicit names like from_local_documents and index_document over hidden behavior.
• Make any test fixture tiny; do not require live SynBioHub access.