Add detailed file index and enhance skill documentation for autopilot, decompose, deploy, plan, and research skills. Introduce tests-only mode in decompose skill, clarify required files for deploy and plan skills, and improve prerequisite checks across skills for better user guidance and workflow efficiency.

_docs/02_document/modules/inference_engine.md

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+# Module: inference_engine
+
+## Purpose
+
+Abstract base class defining the interface that all inference engine implementations must follow.
+
+## Public Interface
+
+### Class: InferenceEngine
+
+#### Fields
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `batch_size` | int | Number of images per inference batch |
+
+#### Methods
+
+| Method | Signature | Description |
+|--------|-----------|-------------|
+| `__init__` | `(bytes model_bytes, int batch_size=1, **kwargs)` | Stores batch_size |
+| `get_input_shape` | `() -> tuple` | Returns (height, width) of model input. Abstract — raises `NotImplementedError` |
+| `get_batch_size` | `() -> int` | Returns `self.batch_size` |
+| `run` | `(input_data) -> list` | Runs inference on preprocessed input blob. Abstract — raises `NotImplementedError` |
+
+## Internal Logic
+
+Pure abstract class. All methods except `get_batch_size` raise `NotImplementedError` and must be overridden by subclasses (`OnnxEngine`, `TensorRTEngine`).
+
+## Dependencies
+
+- **External**: `numpy` (declared in .pxd, not used in base)
+- **Internal**: none (leaf module)
+
+## Consumers
+
+- `onnx_engine` — subclass
+- `tensorrt_engine` — subclass
+- `inference` — type reference in .pxd
+
+## Data Models
+
+None.
+
+## Configuration
+
+None.
+
+## External Integrations
+
+None.
+
+## Security
+
+None.
+
+## Tests
+
+None found.