chore: remove unused python-dotenv dependency and env var remnants

Cleanup after migration to config.yaml (commit 04e3922):
- Remove python-dotenv from requirements.txt (unused in production)
- Remove load_dotenv() imports and calls from test files
- Update test documentation to reference config.yaml instead of old env var names

The production code now only uses CHUNKSILO_CONFIG to locate the config file.
Test-specific env vars (TEST_DATA_DIR, etc.) remain for test isolation.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: Chetic

requirements.txt

@@ -6,7 +6,6 @@ pillow>=10.3.0,<11
 pypdf>=5.1.0,<7
 python-docx>=1.1.0,<2
 mcp>=1.0.0,<2
-python-dotenv>=1.0.0,<2
 huggingface-hub>=0.22.0,<2
 flashrank>=0.1.0,<1
 fastembed>=0.5.0,<1

test/TESTING.md

@@ -63,8 +63,8 @@ python test_retrieval_only.py
 ```
 
 This will:
-- Ingest documents from `DATA_DIR` (default `./data`)
-- Build and persist the index into `STORAGE_DIR` (default `./storage`)
+- Ingest documents from the directories configured in `config.yaml` (default `./data`)
+- Build and persist the index to the storage directory in `config.yaml` (default `./storage`)
 - Perform a retrieval-only test over the index
 
 ### 2. End-to-end retrieval test (MCP server logic)

test/test_rag_metrics.py

@@ -21,9 +21,6 @@
 from urllib.parse import urlparse
 
 import requests
-from dotenv import load_dotenv
-
-load_dotenv()
 
 # Set up logging
 logging.basicConfig(

test/test_retrieval_only.py

@@ -2,7 +2,6 @@
 """Test the RAG system in retrieval-only mode (no LLM in the MCP server)."""
 import traceback
 from pathlib import Path
-from dotenv import load_dotenv
 import pytest
 
 from chunksilo.index import load_index_config, build_index
@@ -11,8 +10,6 @@
 
 STORAGE_DIR = Path(load_config()["storage"]["storage_dir"])
 
-load_dotenv()
-
 
 def test_ingestion():
     """Test the ingestion pipeline."""