[ISSUE-08] Port AssemblyService behind clean SBOL assembly interface

[Gonza10V]

Motivation

• Provide a clean, typed SBOL assembly service that wraps the existing Golden Gate assembly behavior so stages can consume/produce normalized domain records without changing the legacy digestion/ligation internals.
• Keep raw sbol2 objects at the SBOL service boundary and return normalized generated products as IndexedPlasmid records annotated with provenance.

Description

• Added src/buildcompiler/sbol/assembly.py implementing AssemblyJob, AssemblySbolResult, and AssemblyService and private adapter helpers that resolve IndexedPlasmid/IndexedBackbone/IndexedReagent into the legacy shapes expected by sbol2build.Assembly.
• The AssemblyService.run(job: AssemblyJob) -> AssemblySbolResult method adapts normalized inputs, delegates to the existing Assembly implementation from src/buildcompiler/sbol2build.py, preserves SBOL activity/product behavior, and maps legacy products back to IndexedPlasmid with state=MaterialState.GENERATED and provenance metadata.
• Exported the new assembly contracts from src/buildcompiler/sbol/__init__.py so callers can import AssemblyService, AssemblyJob, and AssemblySbolResult alongside SbolResolver.
• Added unit tests tests/unit/sbol/test_assembly_service.py that cover the wrapper contract: a successful run (legacy assembly monkeypatched to isolate the wrapper) and clear ValueError behavior when required SBOL inputs are missing.

Testing

• Import smoke tests: python -c "from buildcompiler.sbol import AssemblyService, AssemblyJob, AssemblySbolResult" and python -c "from buildcompiler.domain import IndexedPlasmid, IndexedBackbone, IndexedReagent" both succeeded.
• Unit tests: pytest tests/unit/sbol and then pytest tests/unit/domain tests/unit/api tests/unit/inventory tests/unit/planning tests/unit/sbol were executed; final run results: 41 passed (all targeted unit tests passed).
• Lint/format (via uv): attempts to run uv run ruff check ., uv run ruff format --check ., and uv run pytest tests/unit/sbol initially failed because uv attempted to fetch the optional SBOLInventory dependency from a git URL and the environment blocked that network fetch (git fetch error / HTTP 403). This is an environment/network failure and not a code failure; local pytest runs succeeded afterwards.

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Codex Task

[Gonza10V]

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Validate plasmid implementation type before returning

When metadata['implementation_identity'] points to an existing non-sbol2.Implementation object (for example a ComponentDefinition), this method returns it without validation because only None triggers the fallback path. That invalid object is then passed into legacy assembly and eventually into part_digestion, which expects an implementation and dereferences .built, causing a runtime failure instead of the wrapper’s intended clear ValueError for bad SBOL inputs.

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