docs: update README, RUN guide, and add CHANGELOG for recent bugfixes and optimizations

CHANGELOG.md

@@ -0,0 +1,29 @@
+# Changelog
+
+All notable changes to the `chicken-counting-sukawarna-det` project are documented in this file.
+
+## [Unreleased] - 2026-08-19
+
+### 🐛 Bug Fixes
+- **Multi-Floor Script Syntax (`run_all_coops.sh`)**:
+  - Resolved fatal `syntax error: unexpected end of file` caused by missing `done` in floor configuration discovery loop.
+  - Expanded config discovery pattern from `K*-L*.yaml` to `*.yaml` to support custom named coops (e.g. `kandang-atas.yaml`).
+- **Excel Report Empty Result Crash (`export_excel_report.py`)**:
+  - Added empty DataFrame pre-check to prevent `IndexError` when exporting reports for dates with no batch runs or newly initialized databases.
+- **Multi-Threaded SQLite Concurrency (`dashboard.py`)**:
+  - Replaced global single `sqlite3` connection with thread-local connections (`threading.local()`) to prevent cursor collision and race conditions across concurrent HTTP worker threads.
+  - Enabled `PRAGMA busy_timeout = 5000` and `PRAGMA journal_mode = WAL` to avoid database lock conflicts during batch processing writes.
+- **Editable Package Installation**:
+  - Configured `pip install -e .` in environment setup to resolve `chicken_counter` imports and enable automatic unit test discovery without manual `PYTHONPATH` prefixes.
+
+### ⚡ Performance & Optimization
+- **Disk Traversal Caching in Live Dashboard (`dashboard.py`)**:
+  - Replaced repetitive `Path.rglob()` scans on every `/api/mortality/*` endpoint with a thread-safe 15-second in-memory TTL cache (`_MORTALITY_CACHE_TTL = 15.0s`).
+  - Added $O(1)$ memory index lookup for serving annotated images (`/api/mortality/image/<filename>`), eliminating full filesystem traversals across 30GB+ video datasets.
+
+### 📁 Configuration & Directory Structure
+- **Floor Configuration & Skeleton Paths**:
+  - Created `configs/floor_config/kandang-atas.yaml` extending `cycle7_batch_optimized.yaml`.
+  - Initialized missing directory skeletons for coops `K1-L1` through `K5-L2` under `../VIDEOS/cycle7/`.
+- **Documentation**:
+  - Updated `README.md` and `RUN.md` with editable install steps and updated project layout.

README.md

@@ -24,8 +24,9 @@ visual.
 
 ```text
 configs/
-  floor_config/                  ← Lightweight floor configs (K1-L1 to K5-L2)
+  floor_config/                  ← Lightweight floor configs (K1-L1 to K5-L2, kandang-atas)
     K1-L1.yaml .. K5-L2.yaml     ← Extends cycle7_batch_optimized.yaml
+    kandang-atas.yaml            ← Extends cycle7_batch_optimized.yaml
   cameras/example_camera.yaml
   cycle7_batch.yaml
   cycle7_batch_optimized.yaml    ← Base batch processing config
@@ -62,6 +63,7 @@ test_run_folder/                 ← Archive of test run scripts and logs
 python3 -m venv venv
 venv/bin/pip install --upgrade pip
 venv/bin/pip install -r requirements.txt
+venv/bin/pip install -e .
 ```
 
 For Jetson deployment you will usually want a Jetson-compatible OpenCV and PyTorch

RUN.md

@@ -22,6 +22,7 @@ cd chicken-counting-sukawarna-det
 python3 -m venv venv
 venv/bin/pip install --upgrade pip
 venv/bin/pip install -r requirements.txt
+venv/bin/pip install -e .
 ```
 
 > **Note**: If moving the project from another machine, always recreate the venv.
@@ -34,8 +35,9 @@ venv/bin/pip install -r requirements.txt
 ```text
 chicken-counting-sukawarna-det/
 ├── configs/
-│   ├── floor_config/                 ← Lightweight floor configs (K1-L1 to K5-L2)
+│   ├── floor_config/                 ← Lightweight floor configs (K1-L1 to K5-L2, kandang-atas)
 │   │   ├── K1-L1.yaml .. K5-L2.yaml  ← Extends cycle7_batch_optimized.yaml
+│   │   └── kandang-atas.yaml         ← Extends cycle7_batch_optimized.yaml
 │   ├── cycle7_batch_optimized.yaml   ← Main base batch processing config
 │   ├── cycle7_batch.yaml             ← Alternate batch config
 │   ├── mortality_config.yaml         ← Mortality (carcass) detection config