Add output_path option to assembly_plan_RDF_to_JSON and update build compiler

[Gonza10V]

Motivation

• Allow callers to control where the assembly-plan JSON is written so downstream steps (zip/simulation) can rely on a known file location instead of a hardcoded output.json.

Description

• Add an optional output_path: str | Path | None parameter to assembly_plan_RDF_to_JSON and write JSON to the provided path, defaulting to output.json when omitted (src/buildcompiler/robotutils.py).
• Update assembly_compiler to call assembly_plan_RDF_to_JSON(..., output_path=f"{files_path}/assemblyplan_output.json") so the zip step uses the generated file (src/buildcompiler/buildcompiler.py).
• Normalize SBOL type checks to use isinstance(file, sbol2.Document) in both robotutils modules and tidy up a now-unused import/assignment in the build compiler.

Testing

• Ran pytest, which executed the test suite but produced network-related failures/errors against external services (proxy blocked access to synbiohub.org / validator.sbolstandard.org), so several tests failed or errored; this is due to external network validation calls, not the JSON output change.
• Ran ruff check src, which passed with no remaining lint errors.

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Codex Task