diff --git a/AGENTS.md b/AGENTS.md
index 2f8abea..0c4ee8a 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -25,9 +25,11 @@ This repository contains DFODE-kit, a Python toolkit for sampling combustion sta
 
 ## Structure
 - `dfode_kit/cli/`: CLI entrypoints and subcommands
-- `dfode_kit/data_operations/`: dataset I/O, labeling, augmentation, integration utilities
-- `dfode_kit/dfode_core/`: models, training, preprocessing
-- `dfode_kit/df_interface/`: DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/cases/`: case init, presets, sampling, and DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/data/`: data contracts, HDF5 I/O, and integration helpers
+- `dfode_kit/data_operations/`: labeling and augmentation workflows
+- `dfode_kit/models/`: model architectures and registries
+- `dfode_kit/training/`: training configuration, loops, and preprocessing
 - `docs/agents/`: deeper agent-facing docs and workflow conventions
 - `tests/`: lightweight harness tests; keep them fast
 
diff --git a/README.md b/README.md
index a23d8e1..763b5d8 100644
--- a/README.md
+++ b/README.md
@@ -133,15 +133,12 @@ If you are working on the repository itself, see:
 
 ## Repository layout
 
-- `dfode_kit/cli/` — canonical CLI entrypoints and subcommands
-- `dfode_kit/cli_tools/` — legacy compatibility shims for older CLI import paths
-- `dfode_kit/cases/` — canonical case init/preset/sampling boundaries for DeepFlame/OpenFOAM workflows
-- `dfode_kit/df_interface/` — legacy compatibility shims for case-facing helpers during the cases migration
-- `dfode_kit/data/` — emerging canonical package for data contracts and HDF5 I/O helpers
-- `dfode_kit/data_operations/` — legacy and transitional dataset I/O, augmentation, labeling, and integration helpers
-- `dfode_kit/models/` — canonical model package
-- `dfode_kit/training/` — canonical training package
-- `dfode_kit/dfode_core/` — legacy compatibility surface for model/training code during migration
+- `dfode_kit/cli/` — CLI entrypoints and subcommands
+- `dfode_kit/cases/` — case init, presets, sampling, and DeepFlame/OpenFOAM-facing helpers
+- `dfode_kit/data/` — data contracts, HDF5 I/O, and integration helpers
+- `dfode_kit/data_operations/` — augmentation and labeling workflows
+- `dfode_kit/models/` — model architectures and registries
+- `dfode_kit/training/` — training configuration, registries, training loops, and preprocessing
 - `canonical_cases/` — canonical flame case templates
 - `tutorials/` — tutorial notebooks and workflow examples
 - `docs/` — published project documentation
diff --git a/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb b/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb
index 8dca223..f24e8b4 100644
--- a/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb
+++ b/canonical_cases/oneD_freely_propagating_flame/dfode_kit_init.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -32,7 +32,7 @@
     "    label_npy,\n",
     "    integrate_h5,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']"
diff --git a/dfode_kit/cli_tools/__init__.py b/dfode_kit/cli_tools/__init__.py
deleted file mode 100644
index 6104fb9..0000000
--- a/dfode_kit/cli_tools/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shims for the renamed ``dfode_kit.cli_tools`` package."""
-
-from dfode_kit.cli import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/command_loader.py b/dfode_kit/cli_tools/command_loader.py
deleted file mode 100644
index 36eba4b..0000000
--- a/dfode_kit/cli_tools/command_loader.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.command_loader`."""
-
-from dfode_kit.cli.command_loader import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/__init__.py b/dfode_kit/cli_tools/commands/__init__.py
deleted file mode 100644
index 21eb97d..0000000
--- a/dfode_kit/cli_tools/commands/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Compatibility shims for :mod:`dfode_kit.cli.commands`."""
diff --git a/dfode_kit/cli_tools/commands/augment.py b/dfode_kit/cli_tools/commands/augment.py
deleted file mode 100644
index 5f4c904..0000000
--- a/dfode_kit/cli_tools/commands/augment.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.augment`."""
-
-from dfode_kit.cli.commands.augment import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/config.py b/dfode_kit/cli_tools/commands/config.py
deleted file mode 100644
index a17f3b7..0000000
--- a/dfode_kit/cli_tools/commands/config.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.config`."""
-
-from dfode_kit.cli.commands.config import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/h52npy.py b/dfode_kit/cli_tools/commands/h52npy.py
deleted file mode 100644
index 1e808f6..0000000
--- a/dfode_kit/cli_tools/commands/h52npy.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.h52npy`."""
-
-from dfode_kit.cli.commands.h52npy import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/init.py b/dfode_kit/cli_tools/commands/init.py
deleted file mode 100644
index a8a7c24..0000000
--- a/dfode_kit/cli_tools/commands/init.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.init`."""
-
-from dfode_kit.cli.commands.init import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/init_helpers.py b/dfode_kit/cli_tools/commands/init_helpers.py
deleted file mode 100644
index 2db40d4..0000000
--- a/dfode_kit/cli_tools/commands/init_helpers.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.init_helpers`."""
-
-from dfode_kit.cli.commands.init_helpers import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/label.py b/dfode_kit/cli_tools/commands/label.py
deleted file mode 100644
index bb1936d..0000000
--- a/dfode_kit/cli_tools/commands/label.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.label`."""
-
-from dfode_kit.cli.commands.label import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/run_case.py b/dfode_kit/cli_tools/commands/run_case.py
deleted file mode 100644
index 494a264..0000000
--- a/dfode_kit/cli_tools/commands/run_case.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.run_case`."""
-
-from dfode_kit.cli.commands.run_case import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/run_case_helpers.py b/dfode_kit/cli_tools/commands/run_case_helpers.py
deleted file mode 100644
index 2b5b87c..0000000
--- a/dfode_kit/cli_tools/commands/run_case_helpers.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.runtime.run_case`."""
-
-from dfode_kit.runtime.run_case import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/sample.py b/dfode_kit/cli_tools/commands/sample.py
deleted file mode 100644
index d2dcd1b..0000000
--- a/dfode_kit/cli_tools/commands/sample.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.sample`."""
-
-from dfode_kit.cli.commands.sample import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/commands/train.py b/dfode_kit/cli_tools/commands/train.py
deleted file mode 100644
index 9f99574..0000000
--- a/dfode_kit/cli_tools/commands/train.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.commands.train`."""
-
-from dfode_kit.cli.commands.train import *  # noqa: F401,F403
diff --git a/dfode_kit/cli_tools/main.py b/dfode_kit/cli_tools/main.py
deleted file mode 100644
index 5732201..0000000
--- a/dfode_kit/cli_tools/main.py
+++ /dev/null
@@ -1,7 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.cli.main`."""
-
-from dfode_kit.cli.main import *  # noqa: F401,F403
-
-
-if __name__ == "__main__":
-    raise SystemExit(main())
diff --git a/dfode_kit/df_interface/__init__.py b/dfode_kit/df_interface/__init__.py
deleted file mode 100644
index 9ae4594..0000000
--- a/dfode_kit/df_interface/__init__.py
+++ /dev/null
@@ -1,31 +0,0 @@
-from importlib import import_module
-
-
-__all__ = [
-    'df_to_h5',
-    'OneDFreelyPropagatingFlameConfig',
-    'setup_one_d_flame_case',
-]
-
-_ATTRIBUTE_MODULES = {
-    'df_to_h5': ('dfode_kit.cases.sampling', 'df_to_h5'),
-    'OneDFreelyPropagatingFlameConfig': (
-        'dfode_kit.cases.presets',
-        'OneDFreelyPropagatingFlameConfig',
-    ),
-    'setup_one_d_flame_case': (
-        'dfode_kit.cases.deepflame',
-        'setup_one_d_flame_case',
-    ),
-}
-
-
-def __getattr__(name):
-    if name not in _ATTRIBUTE_MODULES:
-        raise AttributeError(f"module 'dfode_kit.df_interface' has no attribute '{name}'")
-
-    module_name, attribute_name = _ATTRIBUTE_MODULES[name]
-    module = import_module(module_name)
-    value = getattr(module, attribute_name)
-    globals()[name] = value
-    return value
diff --git a/dfode_kit/df_interface/case_init.py b/dfode_kit/df_interface/case_init.py
deleted file mode 100644
index 17f93ca..0000000
--- a/dfode_kit/df_interface/case_init.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for the future dfode_kit.cases.init module."""
-
-from dfode_kit.cases.init import *  # noqa: F401,F403
diff --git a/dfode_kit/df_interface/flame_configurations.py b/dfode_kit/df_interface/flame_configurations.py
deleted file mode 100644
index dee0353..0000000
--- a/dfode_kit/df_interface/flame_configurations.py
+++ /dev/null
@@ -1,4 +0,0 @@
-"""Compatibility shim for the future dfode_kit.cases.presets module."""
-
-from dfode_kit.cases.presets import *  # noqa: F401,F403
-        
\ No newline at end of file
diff --git a/dfode_kit/df_interface/oneDflame_setup.py b/dfode_kit/df_interface/oneDflame_setup.py
deleted file mode 100755
index d469142..0000000
--- a/dfode_kit/df_interface/oneDflame_setup.py
+++ /dev/null
@@ -1,3 +0,0 @@
-"""Compatibility shim for the future dfode_kit.cases.deepflame module."""
-
-from dfode_kit.cases.deepflame import *  # noqa: F401,F403
diff --git a/dfode_kit/df_interface/sample_case.py b/dfode_kit/df_interface/sample_case.py
deleted file mode 100644
index 57f3b43..0000000
--- a/dfode_kit/df_interface/sample_case.py
+++ /dev/null
@@ -1,4 +0,0 @@
-"""Compatibility shim for the future dfode_kit.cases.sampling module."""
-
-from dfode_kit.cases.sampling import *  # noqa: F401,F403
-
diff --git a/dfode_kit/dfode_core/__init__.py b/dfode_kit/dfode_core/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/dfode_kit/dfode_core/model/__init__.py b/dfode_kit/dfode_core/model/__init__.py
deleted file mode 100644
index 8dd28eb..0000000
--- a/dfode_kit/dfode_core/model/__init__.py
+++ /dev/null
@@ -1,33 +0,0 @@
-"""Compatibility shims for :mod:`dfode_kit.models`."""
-
-from importlib import import_module
-
-
-__all__ = [
-    "MLP",
-    "build_mlp",
-    "create_model",
-    "get_model_factory",
-    "register_model",
-    "registered_models",
-]
-
-_ATTRIBUTE_MODULES = {
-    "MLP": ("dfode_kit.models.mlp", "MLP"),
-    "build_mlp": ("dfode_kit.models.mlp", "build_mlp"),
-    "create_model": ("dfode_kit.models.registry", "create_model"),
-    "get_model_factory": ("dfode_kit.models.registry", "get_model_factory"),
-    "register_model": ("dfode_kit.models.registry", "register_model"),
-    "registered_models": ("dfode_kit.models.registry", "registered_models"),
-}
-
-
-def __getattr__(name):
-    if name not in _ATTRIBUTE_MODULES:
-        raise AttributeError(f"module 'dfode_kit.dfode_core.model' has no attribute '{name}'")
-
-    module_name, attribute_name = _ATTRIBUTE_MODULES[name]
-    module = import_module(module_name)
-    value = getattr(module, attribute_name)
-    globals()[name] = value
-    return value
diff --git a/dfode_kit/dfode_core/model/mlp.py b/dfode_kit/dfode_core/model/mlp.py
deleted file mode 100644
index 03ce898..0000000
--- a/dfode_kit/dfode_core/model/mlp.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.models.mlp`."""
-
-from dfode_kit.models.mlp import MLP, build_mlp
-
-__all__ = ["MLP", "build_mlp"]
diff --git a/dfode_kit/dfode_core/model/registry.py b/dfode_kit/dfode_core/model/registry.py
deleted file mode 100644
index f4fbe08..0000000
--- a/dfode_kit/dfode_core/model/registry.py
+++ /dev/null
@@ -1,10 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.models.registry`."""
-
-from dfode_kit.models.registry import create_model, get_model_factory, register_model, registered_models
-
-__all__ = [
-    "create_model",
-    "get_model_factory",
-    "register_model",
-    "registered_models",
-]
diff --git a/dfode_kit/dfode_core/train/__init__.py b/dfode_kit/dfode_core/train/__init__.py
deleted file mode 100644
index d7a5525..0000000
--- a/dfode_kit/dfode_core/train/__init__.py
+++ /dev/null
@@ -1,43 +0,0 @@
-"""Compatibility shims for :mod:`dfode_kit.training`."""
-
-from importlib import import_module
-
-
-__all__ = [
-    "ModelConfig",
-    "OptimizerConfig",
-    "TrainerConfig",
-    "TrainingConfig",
-    "create_trainer",
-    "default_training_config",
-    "get_trainer_factory",
-    "register_trainer",
-    "registered_trainers",
-    "train",
-    "with_overrides",
-]
-
-_ATTRIBUTE_MODULES = {
-    "ModelConfig": ("dfode_kit.training.config", "ModelConfig"),
-    "OptimizerConfig": ("dfode_kit.training.config", "OptimizerConfig"),
-    "TrainerConfig": ("dfode_kit.training.config", "TrainerConfig"),
-    "TrainingConfig": ("dfode_kit.training.config", "TrainingConfig"),
-    "create_trainer": ("dfode_kit.training.registry", "create_trainer"),
-    "default_training_config": ("dfode_kit.training.config", "default_training_config"),
-    "get_trainer_factory": ("dfode_kit.training.registry", "get_trainer_factory"),
-    "register_trainer": ("dfode_kit.training.registry", "register_trainer"),
-    "registered_trainers": ("dfode_kit.training.registry", "registered_trainers"),
-    "train": ("dfode_kit.training.train", "train"),
-    "with_overrides": ("dfode_kit.training.config", "with_overrides"),
-}
-
-
-def __getattr__(name):
-    if name not in _ATTRIBUTE_MODULES:
-        raise AttributeError(f"module 'dfode_kit.dfode_core.train' has no attribute '{name}'")
-
-    module_name, attribute_name = _ATTRIBUTE_MODULES[name]
-    module = import_module(module_name)
-    value = getattr(module, attribute_name)
-    globals()[name] = value
-    return value
diff --git a/dfode_kit/dfode_core/train/config.py b/dfode_kit/dfode_core/train/config.py
deleted file mode 100644
index 66b7fce..0000000
--- a/dfode_kit/dfode_core/train/config.py
+++ /dev/null
@@ -1,19 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.training.config`."""
-
-from dfode_kit.training.config import (
-    ModelConfig,
-    OptimizerConfig,
-    TrainerConfig,
-    TrainingConfig,
-    default_training_config,
-    with_overrides,
-)
-
-__all__ = [
-    "ModelConfig",
-    "OptimizerConfig",
-    "TrainerConfig",
-    "TrainingConfig",
-    "default_training_config",
-    "with_overrides",
-]
diff --git a/dfode_kit/dfode_core/train/formation.py b/dfode_kit/dfode_core/train/formation.py
deleted file mode 100644
index 20b18ee..0000000
--- a/dfode_kit/dfode_core/train/formation.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.training.formation`."""
-
-from dfode_kit.training.formation import formation_calculate
-
-__all__ = ["formation_calculate"]
diff --git a/dfode_kit/dfode_core/train/registry.py b/dfode_kit/dfode_core/train/registry.py
deleted file mode 100644
index 26011aa..0000000
--- a/dfode_kit/dfode_core/train/registry.py
+++ /dev/null
@@ -1,10 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.training.registry`."""
-
-from dfode_kit.training.registry import create_trainer, get_trainer_factory, register_trainer, registered_trainers
-
-__all__ = [
-    "create_trainer",
-    "get_trainer_factory",
-    "register_trainer",
-    "registered_trainers",
-]
diff --git a/dfode_kit/dfode_core/train/supervised_physics.py b/dfode_kit/dfode_core/train/supervised_physics.py
deleted file mode 100644
index 447392d..0000000
--- a/dfode_kit/dfode_core/train/supervised_physics.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.training.supervised_physics`."""
-
-from dfode_kit.training.supervised_physics import (
-    SupervisedPhysicsTrainer,
-    build_supervised_physics_trainer,
-)
-
-__all__ = ["SupervisedPhysicsTrainer", "build_supervised_physics_trainer"]
diff --git a/dfode_kit/dfode_core/train/train.py b/dfode_kit/dfode_core/train/train.py
deleted file mode 100644
index 7fbcb32..0000000
--- a/dfode_kit/dfode_core/train/train.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""Compatibility shim for :mod:`dfode_kit.training.train`."""
-
-from dfode_kit.training.train import train
-
-__all__ = ["train"]
diff --git a/dfode_kit/runtime_config.py b/dfode_kit/runtime_config.py
deleted file mode 100644
index aad8233..0000000
--- a/dfode_kit/runtime_config.py
+++ /dev/null
@@ -1 +0,0 @@
-from dfode_kit.runtime.config import *  # noqa: F401,F403
diff --git a/dfode_kit/training/__init__.py b/dfode_kit/training/__init__.py
index 8293bf0..92ff2bc 100644
--- a/dfode_kit/training/__init__.py
+++ b/dfode_kit/training/__init__.py
@@ -14,6 +14,7 @@
     "get_trainer_factory",
     "register_trainer",
     "registered_trainers",
+    "DataPreprocessor",
     "train",
 ]
 
@@ -28,6 +29,7 @@
     "get_trainer_factory": ("dfode_kit.training.registry", "get_trainer_factory"),
     "register_trainer": ("dfode_kit.training.registry", "register_trainer"),
     "registered_trainers": ("dfode_kit.training.registry", "registered_trainers"),
+    "DataPreprocessor": ("dfode_kit.training.preprocess", "DataPreprocessor"),
     "train": ("dfode_kit.training.train", "train"),
 }
 
diff --git a/dfode_kit/dfode_core/preprocess.py b/dfode_kit/training/preprocess.py
similarity index 100%
rename from dfode_kit/dfode_core/preprocess.py
rename to dfode_kit/training/preprocess.py
diff --git a/docs/agents/train-config-plan.md b/docs/agents/train-config-plan.md
index 883a144..79c5252 100644
--- a/docs/agents/train-config-plan.md
+++ b/docs/agents/train-config-plan.md
@@ -1,7 +1,7 @@
 # Training/config refactor plan
 
 ## Scope
-Keep changes tightly limited to the model/training package boundary (`dfode_kit/models`, `dfode_kit/training`, plus compatibility shims under `dfode_kit/dfode_core/{model,train}`) and the train CLI surface needed to select registered components. Do not redesign data loading, labeling, or DeepFlame integration in this slice.
+Keep changes tightly limited to the canonical model/training package boundary (`dfode_kit/models`, `dfode_kit/training`) and the train CLI surface needed to select registered components. Do not redesign data loading, labeling, or DeepFlame integration in this slice.
 
 ## Current audit
 - `dfode_kit/training/train.py` hard-codes:
diff --git a/docs/architecture.md b/docs/architecture.md
index 986964a..1e9f36d 100644
--- a/docs/architecture.md
+++ b/docs/architecture.md
@@ -3,10 +3,11 @@
 ## Current repository structure
 
 - `dfode_kit/cli/`: CLI entrypoints and subcommands
-- `dfode_kit/data_operations/`: dataset I/O, contracts, labeling, augmentation, integration utilities
-- `dfode_kit/dfode_core/`: models, training, registries, preprocessing
-- `dfode_kit/cases/`: explicit case init, preset, sampling, and DeepFlame-facing helpers
-- `dfode_kit/df_interface/`: compatibility layer for the legacy case-facing import paths
+- `dfode_kit/cases/`: explicit case init, presets, sampling, and DeepFlame-facing helpers
+- `dfode_kit/data/`: contracts, HDF5 I/O, and integration utilities
+- `dfode_kit/data_operations/`: augmentation and labeling workflows
+- `dfode_kit/models/`: model architectures and registries
+- `dfode_kit/training/`: training configuration, training loops, registries, and preprocessing
 - `docs/agents/`: agent-facing operational and planning docs
 - `tests/`: lightweight repository and harness tests
 
diff --git a/docs/init.md b/docs/init.md
index 81ed8e9..2d1a16a 100644
--- a/docs/init.md
+++ b/docs/init.md
@@ -39,8 +39,6 @@ This preset preserves the current hardcoded empirical logic from:
 - `dfode_kit/cases/presets.py`
 - method: `OneDFreelyPropagatingFlameConfig.update_config()`
 
-Legacy `dfode_kit/df_interface/*` imports remain as compatibility shims during the package-topology migration.
-
 ## Stable intent
 
 The command is a **preset instantiator**, not a claim of universal best practice.
diff --git a/docs/run-case.md b/docs/run-case.md
index b40fc8a..1a5c3d3 100644
--- a/docs/run-case.md
+++ b/docs/run-case.md
@@ -7,7 +7,7 @@ DFODE-kit provides two CLI entrypoints for running DeepFlame/OpenFOAM cases repr
 
 This document is the shared reference for both humans and AI agents.
 
-Implementation note: runtime config helpers now live under `dfode_kit.runtime.config`, and reusable run planning/execution helpers live under `dfode_kit.runtime.run_case`. The legacy import paths remain as compatibility shims during migration.
+Implementation note: runtime config helpers live under `dfode_kit.runtime.config`, and reusable run planning/execution helpers live under `dfode_kit.runtime.run_case`.
 
 ## Why a persistent runtime config exists
 
diff --git a/tests/test_cases_shims.py b/tests/test_cases_shims.py
index 42263b3..9fbb434 100644
--- a/tests/test_cases_shims.py
+++ b/tests/test_cases_shims.py
@@ -1,7 +1,6 @@
 from dfode_kit.cases import init as cases_init
-from dfode_kit.df_interface import case_init as legacy_case_init
 
 
-def test_df_interface_case_init_reexports_cases_symbols():
-    assert legacy_case_init.resolve_oxidizer is cases_init.resolve_oxidizer
-    assert legacy_case_init.DEFAULT_ONE_D_FLAME_PRESET == cases_init.DEFAULT_ONE_D_FLAME_PRESET
+def test_cases_init_exports_expected_symbols():
+    assert callable(cases_init.resolve_oxidizer)
+    assert cases_init.DEFAULT_ONE_D_FLAME_PRESET == "premixed-defaults-v1"
diff --git a/tests/test_cli_main.py b/tests/test_cli_main.py
index 2caa36e..1801ae8 100644
--- a/tests/test_cli_main.py
+++ b/tests/test_cli_main.py
@@ -140,9 +140,8 @@ def test_main_returns_two_for_missing_handler(monkeypatch, capsys):
     assert "Unknown command: dummy" in captured.err
 
 
-def test_cli_tools_command_loader_shim_re_exports_cli_symbols():
-    shim = import_module("dfode_kit.cli_tools.command_loader")
+def test_cli_command_loader_module_is_importable():
     direct = import_module("dfode_kit.cli.command_loader")
 
-    assert shim.load_command_specs is direct.load_command_specs
-    assert shim.load_command is direct.load_command
+    assert callable(direct.load_command_specs)
+    assert callable(direct.load_command)
diff --git a/tests/test_run_case_cli.py b/tests/test_run_case_cli.py
index bb69329..12de4fe 100644
--- a/tests/test_run_case_cli.py
+++ b/tests/test_run_case_cli.py
@@ -86,9 +86,6 @@ def fake_run(command, stdout=None, stderr=None, text=None):
     assert calls['command'] == ['bash', '-lc', 'echo hello']
 
 
-
-def test_legacy_run_case_helpers_shim_matches_new_module():
-    from dfode_kit.cli_tools.commands import run_case_helpers as legacy_run_case_helpers
-
-    assert legacy_run_case_helpers.resolve_run_case_plan is run_case_helpers.resolve_run_case_plan
-    assert legacy_run_case_helpers.execute_run_case is run_case_helpers.execute_run_case
+def test_run_case_helpers_module_is_importable_from_runtime_package():
+    assert callable(run_case_helpers.resolve_run_case_plan)
+    assert callable(run_case_helpers.execute_run_case)
diff --git a/tests/test_runtime_config.py b/tests/test_runtime_config.py
index b005b5f..67e17f1 100644
--- a/tests/test_runtime_config.py
+++ b/tests/test_runtime_config.py
@@ -27,8 +27,6 @@ def test_validate_config_key_rejects_unknown():
         raise AssertionError('expected ValueError')
 
 
-def test_legacy_runtime_config_shim_matches_new_module():
-    from dfode_kit import runtime_config as legacy_runtime_config
-
-    assert legacy_runtime_config.get_config_path is runtime_config.get_config_path
-    assert legacy_runtime_config.resolve_runtime_config is runtime_config.resolve_runtime_config
+def test_runtime_config_module_exports_expected_helpers():
+    assert callable(runtime_config.get_config_path)
+    assert callable(runtime_config.resolve_runtime_config)
diff --git a/tests/test_train_config_architecture.py b/tests/test_train_config_architecture.py
index f7502ae..971dc43 100644
--- a/tests/test_train_config_architecture.py
+++ b/tests/test_train_config_architecture.py
@@ -81,17 +81,14 @@ def test_registry_errors_include_available_names():
     assert "Unknown model 'does_not_exist'" in str(excinfo.value)
 
 
-def test_legacy_dfode_core_imports_remain_available_as_shims():
+def test_canonical_training_and_model_modules_are_importable():
     canonical_config = import_module("dfode_kit.training.config")
     canonical_model_registry = import_module("dfode_kit.models.registry")
     canonical_trainer_registry = import_module("dfode_kit.training.registry")
-    legacy_config = import_module("dfode_kit.dfode_core.train.config")
-    legacy_model_registry = import_module("dfode_kit.dfode_core.model.registry")
-    legacy_trainer_registry = import_module("dfode_kit.dfode_core.train.registry")
 
-    assert legacy_config.TrainingConfig is canonical_config.TrainingConfig
-    assert legacy_model_registry.register_model is canonical_model_registry.register_model
-    assert legacy_trainer_registry.register_trainer is canonical_trainer_registry.register_trainer
+    assert canonical_config.TrainingConfig is not None
+    assert callable(canonical_model_registry.register_model)
+    assert callable(canonical_trainer_registry.register_trainer)
 
 
 def test_training_plan_doc_exists_and_mentions_registry_design():
diff --git a/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_init.ipynb b/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_init.ipynb
index cf27849..3bdda39 100644
--- a/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_init.ipynb
+++ b/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_init.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -32,7 +32,7 @@
     "    label_npy,\n",
     "    integrate_h5,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']"
diff --git a/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_tutorial.ipynb b/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_tutorial.ipynb
index 5ad9be5..8d0be27 100644
--- a/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_tutorial.ipynb
+++ b/tutorials/oneD_freely_propagating_flame/1_sample_train/dfode_kit_tutorial.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -33,7 +33,7 @@
     "    integrate_h5,\n",
     "    calculate_error,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']\n",
@@ -250,7 +250,7 @@
    "source": [
     "import torch\n",
     "import cantera as ct\n",
-    "from dfode_kit.dfode_core.train.formation import formation_calculate\n",
+    "from dfode_kit.training.formation import formation_calculate\n",
     "\n",
     "source_file = 'dataset.npy'\n",
     "time_step = 1e-06\n",
diff --git a/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_init.ipynb b/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_init.ipynb
index ca59f50..2790b23 100644
--- a/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_init.ipynb
+++ b/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_init.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -32,7 +32,7 @@
     "    label_npy,\n",
     "    integrate_h5,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']"
diff --git a/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_tutorial.ipynb b/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_tutorial.ipynb
index 917344b..5d5d347 100644
--- a/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_tutorial.ipynb
+++ b/tutorials/twoD_HIT_flame/1_sample_train/dfode_kit_tutorial.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from dfode_kit.df_interface import (\n",
+    "from dfode_kit.cases import (\n",
     "    OneDFreelyPropagatingFlameConfig,\n",
     "    setup_one_d_flame_case,\n",
     "    df_to_h5,\n",
@@ -33,7 +33,7 @@
     "    integrate_h5,\n",
     "    calculate_error,\n",
     ")\n",
-    "from dfode_kit.dfode_core.model.mlp import MLP\n",
+    "from dfode_kit.models.mlp import MLP\n",
     "from dfode_kit.utils import BCT\n",
     "\n",
     "DFODE_ROOT = os.environ['DFODE_ROOT']\n",
@@ -257,7 +257,7 @@
    "source": [
     "import torch\n",
     "import cantera as ct\n",
-    "from dfode_kit.dfode_core.train.formation import formation_calculate\n",
+    "from dfode_kit.training.formation import formation_calculate\n",
     "\n",
     "source_file = 'dataset.npy'\n",
     "time_step = 1e-06\n",