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)