diff --git a/src/buildcompiler/adapters/__init__.py b/src/buildcompiler/adapters/__init__.py
index 5e19692..3390756 100644
--- a/src/buildcompiler/adapters/__init__.py
+++ b/src/buildcompiler/adapters/__init__.py
@@ -1 +1,5 @@
-"""Package scaffolding for clean architecture."""
+"""Adapter package exports without optional dependency side effects."""
+
+from .protocols import ProtocolArtifact, maybe_write_protocol_artifacts
+
+__all__ = ["ProtocolArtifact", "maybe_write_protocol_artifacts"]
diff --git a/src/buildcompiler/adapters/opentrons/__init__.py b/src/buildcompiler/adapters/opentrons/__init__.py
index 5e19692..48db553 100644
--- a/src/buildcompiler/adapters/opentrons/__init__.py
+++ b/src/buildcompiler/adapters/opentrons/__init__.py
@@ -1 +1,13 @@
-"""Package scaffolding for clean architecture."""
+"""Optional Opentrons adapter exports."""
+
+from .simulation import (
+    OpentronsSimulationAdapter,
+    OptionalAutomationDependencyError,
+    SimulationResult,
+)
+
+__all__ = [
+    "OpentronsSimulationAdapter",
+    "OptionalAutomationDependencyError",
+    "SimulationResult",
+]
diff --git a/src/buildcompiler/adapters/opentrons/simulation.py b/src/buildcompiler/adapters/opentrons/simulation.py
new file mode 100644
index 0000000..a8c8e17
--- /dev/null
+++ b/src/buildcompiler/adapters/opentrons/simulation.py
@@ -0,0 +1,44 @@
+"""Optional Opentrons simulation boundary adapter."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from pathlib import Path
+
+from buildcompiler.api import ProtocolOptions
+
+
+class OptionalAutomationDependencyError(ImportError):
+    """Raised when optional automation dependency is unavailable."""
+
+
+@dataclass
+class SimulationResult:
+    ran: bool
+    logs: list[str] = field(default_factory=list)
+    metadata: dict[str, object] = field(default_factory=dict)
+
+
+class OpentronsSimulationAdapter:
+    def simulate(
+        self, protocol_source: str | Path, *, options: ProtocolOptions
+    ) -> SimulationResult:
+        if not options.simulate:
+            return SimulationResult(
+                ran=False,
+                logs=["Simulation skipped: ProtocolOptions.simulate is False."],
+                metadata={"protocol_source": str(protocol_source)},
+            )
+
+        try:
+            __import__("opentrons")
+        except ImportError as exc:
+            raise OptionalAutomationDependencyError(
+                "Install synbio-buildcompiler[automation] to use Opentrons simulation."
+            ) from exc
+
+        return SimulationResult(
+            ran=True,
+            logs=["Simulation dependency check passed."],
+            metadata={"protocol_source": str(protocol_source)},
+        )
diff --git a/src/buildcompiler/adapters/protocols.py b/src/buildcompiler/adapters/protocols.py
new file mode 100644
index 0000000..92c8e7b
--- /dev/null
+++ b/src/buildcompiler/adapters/protocols.py
@@ -0,0 +1,55 @@
+"""Protocol artifact boundaries for optional file output."""
+
+from __future__ import annotations
+
+import json
+from dataclasses import dataclass, field
+from pathlib import Path
+
+from buildcompiler.api import ProtocolMode, ProtocolOptions
+
+
+@dataclass
+class ProtocolArtifact:
+    kind: str
+    path: Path | None = None
+    content: str | dict[str, object] | list[dict[str, object]] | None = None
+    metadata: dict[str, object] = field(default_factory=dict)
+
+
+def _artifact_filename(*, basename: str, kind: str) -> str:
+    safe_kind = kind.replace(" ", "_").lower()
+    return f"{basename}_{safe_kind}.json"
+
+
+def maybe_write_protocol_artifacts(
+    *,
+    payloads: dict[str, object],
+    options: ProtocolOptions,
+    basename: str = "buildcompiler_protocol",
+) -> dict[str, ProtocolArtifact]:
+    """Return in-memory protocol payloads and optionally write them to disk."""
+
+    should_write = (
+        options.mode in {ProtocolMode.MANUAL, ProtocolMode.AUTOMATED}
+        and options.results_dir is not None
+    )
+    output_dir = Path(options.results_dir) if should_write else None
+    if output_dir is not None:
+        output_dir.mkdir(parents=True, exist_ok=True)
+
+    artifacts: dict[str, ProtocolArtifact] = {}
+    for kind, payload in payloads.items():
+        artifact = ProtocolArtifact(kind=kind, content=payload)
+        if output_dir is not None:
+            path = output_dir / _artifact_filename(basename=basename, kind=kind)
+            path.write_text(
+                json.dumps(payload, indent=2, sort_keys=True), encoding="utf-8"
+            )
+            artifact.path = path
+            artifact.metadata["written"] = True
+        else:
+            artifact.metadata["written"] = False
+        artifacts[kind] = artifact
+
+    return artifacts
diff --git a/src/buildcompiler/adapters/pudu/__init__.py b/src/buildcompiler/adapters/pudu/__init__.py
index a31fbde..50838bf 100644
--- a/src/buildcompiler/adapters/pudu/__init__.py
+++ b/src/buildcompiler/adapters/pudu/__init__.py
@@ -1,5 +1,16 @@
 """PUDU adapter exports."""
 
 from .assembly_json import assembly_route_to_pudu_json, assembly_routes_to_pudu_json
+from .plating_json import plating_to_pudu_json
+from .transformation_json import (
+    transformation_to_pudu_json,
+    transformations_to_pudu_json,
+)
 
-__all__ = ["assembly_route_to_pudu_json", "assembly_routes_to_pudu_json"]
+__all__ = [
+    "assembly_route_to_pudu_json",
+    "assembly_routes_to_pudu_json",
+    "transformation_to_pudu_json",
+    "transformations_to_pudu_json",
+    "plating_to_pudu_json",
+]
diff --git a/src/buildcompiler/adapters/pudu/plating_json.py b/src/buildcompiler/adapters/pudu/plating_json.py
new file mode 100644
index 0000000..3648e20
--- /dev/null
+++ b/src/buildcompiler/adapters/pudu/plating_json.py
@@ -0,0 +1,22 @@
+"""In-memory adapter for compiler-level PUDU plating JSON payloads."""
+
+from collections import OrderedDict
+from collections.abc import Mapping
+from typing import Any
+
+
+def plating_to_pudu_json(
+    *,
+    bacterium_locations: Mapping[str, str],
+    advanced_parameters: Mapping[str, object] | None = None,
+) -> dict[str, object]:
+    """Adapt plating records into deterministic legacy-compatible PUDU JSON keys."""
+
+    stable_locations = OrderedDict(
+        sorted(bacterium_locations.items(), key=lambda kv: kv[0])
+    )
+    payload: dict[str, Any] = {
+        "bacterium_locations": dict(stable_locations),
+        "advanced_parameters": dict(advanced_parameters or {}),
+    }
+    return payload
diff --git a/src/buildcompiler/adapters/pudu/transformation_json.py b/src/buildcompiler/adapters/pudu/transformation_json.py
new file mode 100644
index 0000000..207a561
--- /dev/null
+++ b/src/buildcompiler/adapters/pudu/transformation_json.py
@@ -0,0 +1,53 @@
+"""In-memory adapter for compiler-level PUDU transformation JSON payloads."""
+
+from collections.abc import Sequence
+
+from buildcompiler.domain import IndexedPlasmid
+
+
+def _stable_identifier(identity: str, display_id: str | None) -> str:
+    return identity or display_id or ""
+
+
+def _plasmid_identifier(plasmid: IndexedPlasmid | str) -> str:
+    if isinstance(plasmid, str):
+        return plasmid
+    return _stable_identifier(identity=plasmid.identity, display_id=plasmid.display_id)
+
+
+def transformation_to_pudu_json(
+    *,
+    strain_identity: str,
+    chassis_identity: str,
+    plasmids: Sequence[IndexedPlasmid | str],
+) -> dict[str, object]:
+    """Adapt a transformation record into legacy-compatible PUDU JSON keys."""
+
+    return {
+        "Strain": strain_identity,
+        "Chassis": chassis_identity,
+        "Plasmids": [_plasmid_identifier(plasmid) for plasmid in plasmids],
+    }
+
+
+def transformations_to_pudu_json(
+    *,
+    strain_identities: Sequence[str],
+    chassis_identities: Sequence[str],
+    plasmid_sets: Sequence[Sequence[IndexedPlasmid | str]],
+) -> list[dict[str, object]]:
+    """Batch helper for deterministic in-memory transformation JSON payloads."""
+
+    return [
+        transformation_to_pudu_json(
+            strain_identity=strain_identity,
+            chassis_identity=chassis_identity,
+            plasmids=plasmids,
+        )
+        for strain_identity, chassis_identity, plasmids in zip(
+            strain_identities,
+            chassis_identities,
+            plasmid_sets,
+            strict=True,
+        )
+    ]
diff --git a/tests/unit/adapters/opentrons/test_simulation_boundary.py b/tests/unit/adapters/opentrons/test_simulation_boundary.py
new file mode 100644
index 0000000..53fbf2c
--- /dev/null
+++ b/tests/unit/adapters/opentrons/test_simulation_boundary.py
@@ -0,0 +1,38 @@
+import builtins
+import sys
+
+import pytest
+
+from buildcompiler.adapters.opentrons import (
+    OpentronsSimulationAdapter,
+    OptionalAutomationDependencyError,
+)
+from buildcompiler.api import ProtocolOptions
+
+
+def test_opentrons_import_is_lazy():
+    assert "opentrons" not in sys.modules
+
+
+def test_simulate_false_does_not_import_opentrons():
+    adapter = OpentronsSimulationAdapter()
+
+    result = adapter.simulate("protocol.py", options=ProtocolOptions(simulate=False))
+
+    assert result.ran is False
+    assert "opentrons" not in sys.modules
+
+
+def test_simulate_true_missing_dependency_raises(monkeypatch):
+    adapter = OpentronsSimulationAdapter()
+
+    real_import = builtins.__import__
+
+    def fake_import(name, *args, **kwargs):
+        if name == "opentrons":
+            raise ImportError("forced missing dependency")
+        return real_import(name, *args, **kwargs)
+
+    monkeypatch.setattr(builtins, "__import__", fake_import)
+    with pytest.raises(OptionalAutomationDependencyError):
+        adapter.simulate("protocol.py", options=ProtocolOptions(simulate=True))
diff --git a/tests/unit/adapters/pudu/test_plating_json.py b/tests/unit/adapters/pudu/test_plating_json.py
new file mode 100644
index 0000000..aa075e5
--- /dev/null
+++ b/tests/unit/adapters/pudu/test_plating_json.py
@@ -0,0 +1,19 @@
+from buildcompiler.adapters.pudu import plating_to_pudu_json
+
+
+def test_plating_to_pudu_json_shape_and_values():
+    payload = plating_to_pudu_json(
+        bacterium_locations={"strain_b": "B2", "strain_a": "A1"},
+        advanced_parameters={"replicates": 2},
+    )
+
+    assert payload == {
+        "bacterium_locations": {"strain_a": "A1", "strain_b": "B2"},
+        "advanced_parameters": {"replicates": 2},
+    }
+
+
+def test_plating_to_pudu_json_defaults_advanced_parameters():
+    payload = plating_to_pudu_json(bacterium_locations={"strain_a": "A1"})
+
+    assert payload["advanced_parameters"] == {}
diff --git a/tests/unit/adapters/pudu/test_transformation_json.py b/tests/unit/adapters/pudu/test_transformation_json.py
new file mode 100644
index 0000000..d18f7ab
--- /dev/null
+++ b/tests/unit/adapters/pudu/test_transformation_json.py
@@ -0,0 +1,38 @@
+from buildcompiler.adapters.pudu import (
+    transformation_to_pudu_json,
+    transformations_to_pudu_json,
+)
+from buildcompiler.domain import IndexedPlasmid
+
+
+def test_transformation_to_pudu_json_shape_and_values():
+    payload = transformation_to_pudu_json(
+        strain_identity="https://example.org/strain/s1",
+        chassis_identity="https://example.org/chassis/c1",
+        plasmids=[
+            IndexedPlasmid(identity="https://example.org/plasmids/p1"),
+            "https://example.org/plasmids/p2",
+        ],
+    )
+
+    assert payload == {
+        "Strain": "https://example.org/strain/s1",
+        "Chassis": "https://example.org/chassis/c1",
+        "Plasmids": [
+            "https://example.org/plasmids/p1",
+            "https://example.org/plasmids/p2",
+        ],
+    }
+
+
+def test_transformations_to_pudu_json_batch_helper_is_deterministic():
+    payloads = transformations_to_pudu_json(
+        strain_identities=["s1", "s2"],
+        chassis_identities=["c1", "c2"],
+        plasmid_sets=[["p1"], ["p2", "p3"]],
+    )
+
+    assert payloads == [
+        {"Strain": "s1", "Chassis": "c1", "Plasmids": ["p1"]},
+        {"Strain": "s2", "Chassis": "c2", "Plasmids": ["p2", "p3"]},
+    ]
diff --git a/tests/unit/adapters/test_protocol_boundaries.py b/tests/unit/adapters/test_protocol_boundaries.py
new file mode 100644
index 0000000..266dbf6
--- /dev/null
+++ b/tests/unit/adapters/test_protocol_boundaries.py
@@ -0,0 +1,38 @@
+from buildcompiler.adapters import maybe_write_protocol_artifacts
+from buildcompiler.api import ProtocolMode, ProtocolOptions
+
+
+def test_protocol_mode_none_returns_in_memory_only(tmp_path):
+    artifacts = maybe_write_protocol_artifacts(
+        payloads={"assembly": {"k": "v"}},
+        options=ProtocolOptions(mode=ProtocolMode.NONE, results_dir=tmp_path),
+        basename="artifact",
+    )
+
+    assert artifacts["assembly"].path is None
+    assert artifacts["assembly"].content == {"k": "v"}
+    assert artifacts["assembly"].metadata["written"] is False
+    assert not any(tmp_path.iterdir())
+
+
+def test_protocol_mode_manual_writes_when_results_dir_set(tmp_path):
+    artifacts = maybe_write_protocol_artifacts(
+        payloads={"assembly": {"k": "v"}},
+        options=ProtocolOptions(mode=ProtocolMode.MANUAL, results_dir=tmp_path),
+        basename="artifact",
+    )
+
+    path = artifacts["assembly"].path
+    assert path is not None
+    assert path.name == "artifact_assembly.json"
+    assert path.exists()
+
+
+def test_protocol_mode_automated_with_no_results_dir_writes_nothing():
+    artifacts = maybe_write_protocol_artifacts(
+        payloads={"plating": {"k": "v"}},
+        options=ProtocolOptions(mode=ProtocolMode.AUTOMATED, results_dir=None),
+    )
+
+    assert artifacts["plating"].path is None
+    assert artifacts["plating"].metadata["written"] is False
diff --git a/tests/unit/test_core_imports.py b/tests/unit/test_core_imports.py
new file mode 100644
index 0000000..f5440d5
--- /dev/null
+++ b/tests/unit/test_core_imports.py
@@ -0,0 +1,21 @@
+import sys
+
+
+def test_core_imports_do_not_load_optional_automation_dependencies():
+    import buildcompiler
+    from buildcompiler.adapters.opentrons import OpentronsSimulationAdapter
+    from buildcompiler.adapters.pudu import (
+        plating_to_pudu_json,
+        transformation_to_pudu_json,
+    )
+    from buildcompiler.api import BuildOptions
+
+    assert buildcompiler
+    assert BuildOptions
+    assert OpentronsSimulationAdapter
+    assert transformation_to_pudu_json
+    assert plating_to_pudu_json
+
+    assert "pudupy" not in sys.modules
+    assert "opentrons" not in sys.modules
+    assert "SBOLInventory" not in sys.modules