Update docs with new directory structure

- Updated AGENTS.md and README.md to reflect:
  - Removal of motia-backend
  - Moving bttoxin_digger_v5_repro to tools/reproduction/
  - Added crispr_cas to structure

AGENTS.md

@@ -162,6 +162,9 @@ bttoxin-pipeline/
 │   └── toxicity-data.csv        # BPPRC specificity data
 ├── external_dbs/                # Optional external database
 │   └── bt_toxin/                # Updated BtToxin database
+├── tools/                       # Utility tools and environments
+│   └── reproduction/            # Reproduction environments
+│       └── bttoxin_digger/      # BtToxin_Digger reproduction env
 ├── tests/                       # Test suite
 │   ├── test_pixi_runner.py      # Property-based tests
 │   └── test_data/               # Test input files (.fna)

README.md

@@ -370,13 +370,17 @@ bttoxin-pipeline/
 │   └── toxicity-data.csv     # BPPRC specificity data
 ├── external_dbs/             # External databases (optional)
 │   └── bt_toxin/             # Updated BtToxin database
+├── tools/                    # Utility tools and environments
+│   └── reproduction/         # BtToxin_Digger reproduction env
+│       └── bttoxin_digger/
 ├── tests/                    # Test suite
 │   ├── test_pixi_runner.py   # Property-based tests
 │   └── test_data/            # Test input files
 ├── docs/                     # Documentation
 ├── runs/                     # Pipeline outputs (gitignored)
 ├── backend/                  # FastAPI backend (optional web service)
-└── frontend/                 # Vue.js frontend (optional web UI)
+├── frontend/                 # Vue.js frontend (optional web UI)
+└── crispr_cas/               # CRISPR-Cas analysis module
 ```
 
 ## Docker Deployment