[SPRINT-02-05] Consolidate Plasmid model and remove duplicate wrapper logic

[Gonza10V]

Parent sprint: #87
Depends on: #88, #89, #90, #91
Recommended order: 5
Codex-ready: yes

Goal

Make buildcompiler.plasmid.Plasmid the single runtime wrapper for indexed plasmids/backbones and remove or deprecate the duplicate Plasmid class in abstract_translator.py.

Background

The current codebase has at least two Plasmid concepts:

• src/buildcompiler/plasmid.py defines Plasmid with plasmid_definition, strain/plasmid implementations, fusion sites, name, and antibiotic resistance.
• src/buildcompiler/abstract_translator.py also defines a Plasmid wrapper with a different constructor and fields.

This increases the risk that indexing, compatibility matching, assembly, and transformation disagree on object shape, fusion-site ordering, antibiotic detection, or equality semantics.

Scope

• Choose buildcompiler.plasmid.Plasmid as the canonical runtime wrapper.
• Update abstract_translator.py helpers to import and use the canonical Plasmid, or rename the old helper class to avoid runtime confusion if it cannot yet be removed.
• Add tests for canonical Plasmid construction from fixture SBOL objects.
• Add tests for fusion-site extraction, antibiotic resistance extraction, equality, hashing, and repr/debug output.
• Ensure assembly code still accepts the canonical Plasmid object.

Non-goals

• Do not redesign the entire inventory system.
• Do not change SBOL biological semantics unless current tests prove the old behavior was wrong.
• Do not rewrite Assembly internals in this issue.

Acceptance criteria

• There is one canonical Plasmid wrapper used by indexing, route selection, and assembly paths.
• abstract_translator.py no longer defines a conflicting runtime Plasmid class, or it is clearly renamed/private and not used by active runtime paths.
• Fusion-site matching is covered by tests using fixture SBOL.
• Antibiotic detection is covered by tests using fixture SBOL.
• Equality/hash behavior uses stable SBOL identity semantics.
• Existing assembly path still runs with the canonical object shape.

Verification

Run:

pytest -k "plasmid or fusion or antibiotic or assembly"
ruff check .

Codex implementation notes

• Keep this as a mechanical consolidation PR where possible.
• If old code paths are unused, remove them with tests proving the active path still works.
• If old code paths are still used, update them incrementally rather than making a giant rewrite.
• Prefer identities/display IDs in assertions rather than raw object equality where SBOL object identity is unstable.