Add clean-architecture package scaffolding (issue #53)

[Gonza10V]

Motivation

• Provide the package structure required by the clean-architecture rewrite (ADR-001 / ARCHITECTURE.md) so future milestones can implement domain contracts, planners, stages, execution, adapters, and reporting without changing the root package name buildcompiler.
• Keep the change strictly scaffolding-only: no behavior, no compatibility wrappers, and no optional automation dependencies imported from core packages.

Description

• Added package markers (__init__.py) for the new clean-architecture layout: api, domain, planning, execution, stages, sbol, inventory, adapters, adapters.pudu, adapters.opentrons, and reporting under src/buildcompiler/.
• Added a small import smoke test tests/test_package_scaffolding.py that imports each new package to validate that core imports resolve without pulling optional automation dependencies.
• All new __init__.py files are minimal placeholders (module docstrings only) to avoid introducing behavior or external dependencies.

Testing

• Ran PYTHONPATH=src python -c "import buildcompiler" and PYTHONPATH=src python -c "import buildcompiler.api; import buildcompiler.domain; import buildcompiler.planning; import buildcompiler.execution; import buildcompiler.stages; import buildcompiler.sbol; import buildcompiler.inventory; import buildcompiler.adapters; import buildcompiler.adapters.pudu; import buildcompiler.adapters.opentrons; import buildcompiler.reporting", both of which succeeded (imports resolved from src).
• Ran PYTHONPATH=src pytest tests/test_package_scaffolding.py and the single import-smoke test passed (1 passed).
• Attempted uv run ruff check . but the run failed during environment preparation due to a network/git fetch error for an optional dependency (SBOLInventory), so uv-based linting could not complete in this environment; running ruff check . without uv was attempted but revealed pre-existing lint issues outside the scope of this scaffolding PR.
• Assumptions and follow-up: local import validation with PYTHONPATH=src is acceptable for this scaffolding step; next work items are issue [ISSUE-02] Implement domain enums and result dataclasses #54 (domain enums/dataclasses) followed by [ISSUE-03] Implement BuildOptions option groups #55 (BuildOptions) and no behavioral work is included here.

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Codex Task

[Gonza10V]

closes #52