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/annotation.md

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+# Module: annotation
+
+## Purpose
+
+Data models for object detections and annotations (grouped detections for a frame/tile with metadata).
+
+## Public Interface
+
+### Class: Detection
+
+Represents a single bounding box detection in normalized coordinates.
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `x` | double | Center X (normalized 0..1) |
+| `y` | double | Center Y (normalized 0..1) |
+| `w` | double | Width (normalized 0..1) |
+| `h` | double | Height (normalized 0..1) |
+| `cls` | int | Class ID (maps to constants_inf.annotations_dict) |
+| `confidence` | double | Detection confidence (0..1) |
+| `annotation_name` | str | Parent annotation name (set after construction) |
+
+| Method | Signature | Description |
+|--------|-----------|-------------|
+| `__init__` | `(double x, y, w, h, int cls, double confidence)` | Constructor |
+| `__str__` | `() -> str` | Format: `"{cls}: {x} {y} {w} {h}, prob: {confidence}%"` |
+| `__eq__` | `(other) -> bool` | Two detections are equal if all bbox coordinates differ by less than `TILE_DUPLICATE_CONFIDENCE_THRESHOLD` |
+| `overlaps` | `(Detection det2, float confidence_threshold) -> bool` | Returns True if IoU-like overlap ratio (overlap area / min area) exceeds threshold |
+
+### Class: Annotation
+
+Groups detections for a single frame or image tile.
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `name` | str | Unique annotation name (encodes tile/time info) |
+| `original_media_name` | str | Source media filename (without extension/spaces) |
+| `time` | long | Timestamp in milliseconds (video) or 0 (image) |
+| `detections` | list[Detection] | Detections found in this frame/tile |
+| `image` | bytes | JPEG-encoded frame image (set after validation) |
+
+| Method | Signature | Description |
+|--------|-----------|-------------|
+| `__init__` | `(str name, str original_media_name, long ms, list[Detection] detections)` | Sets annotation_name on all detections |
+| `__str__` | `() -> str` | Formatted detection summary |
+| `serialize` | `() -> bytes` | Msgpack serialization with compact keys **(legacy — not called in current codebase)** |
+
+## Internal Logic
+
+- `Detection.__eq__` uses `constants_inf.TILE_DUPLICATE_CONFIDENCE_THRESHOLD` (0.01) to determine if two detections at absolute coordinates are duplicates across adjacent tiles.
+- `Detection.overlaps` computes the overlap as `overlap_area / min(area1, area2)` — this is not standard IoU but a containment-biased metric.
+- `Annotation.__init__` sets `annotation_name` on every child detection.
+
+## Dependencies
+
+- **External**: `msgpack`
+- **Internal**: `constants_inf` (TILE_DUPLICATE_CONFIDENCE_THRESHOLD constant)
+
+## Consumers
+
+- `inference` — creates Detection and Annotation instances during postprocessing, uses overlaps for NMS, uses equality for tile dedup
+- `main` — reads Detection fields for DTO conversion
+
+## Data Models
+
+- `Detection` — bounding box + class + confidence
+- `Annotation` — frame/tile container for detections + metadata + image
+
+## Configuration
+
+None.
+
+## External Integrations
+
+None.
+
+## Security
+
+None.
+
+## Tests
+
+None found.