refactor: reorganize repository to src/ layout

Move 6 packages (core, config, data_processing, analysis, visualization, cli)
into src/ to reduce root clutter. Merge tools/data.py into
data_processing/transforms.py. Move docs to docs/.

Path resolution via .pth file (setup_dev.py), pytest pythonpath config,
and sys.path bootstrap in rxconfig.py and CLI entry points.

Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python).
Fix tomllib import for Python 3.10 compatibility.

All 113 tests pass.

core/logging_config.py

@@ -1,121 +0,0 @@
-"""
-Logging configuration for NHS High-Cost Drug Patient Pathway Analysis Tool.
-
-Provides structured logging setup with console and optional file handlers.
-"""
-
-import logging
-import sys
-from datetime import datetime
-from pathlib import Path
-from typing import Optional
-
-
-# Default log format: timestamp, level, module name, message
-DEFAULT_FORMAT = "%(asctime)s [%(levelname)s] %(name)s: %(message)s"
-DEFAULT_DATE_FORMAT = "%Y-%m-%d %H:%M:%S"
-
-# Simplified format for console output (used when redirecting to GUI)
-SIMPLE_FORMAT = "%(message)s"
-
-
-def setup_logging(
-    level: int = logging.INFO,
-    log_dir: Optional[Path] = None,
-    console: bool = True,
-    file_logging: bool = False,
-    simple_console: bool = False,
-) -> logging.Logger:
-    """
-    Configure application-wide logging.
-
-    Args:
-        level: Logging level (default: INFO)
-        log_dir: Directory for log files (default: ./logs/)
-        console: Whether to log to console/stdout (default: True)
-        file_logging: Whether to log to file (default: False)
-        simple_console: Use simplified format for console (just message, no timestamp)
-
-    Returns:
-        Root logger configured for the application
-
-    Usage:
-        # Basic setup - console only
-        logger = setup_logging()
-
-        # With file logging
-        logger = setup_logging(file_logging=True)
-
-        # Debug mode
-        logger = setup_logging(level=logging.DEBUG)
-
-        # GUI mode - simple format for stdout capture
-        logger = setup_logging(simple_console=True)
-    """
-    # Get root logger for the application
-    root_logger = logging.getLogger("pathways")
-
-    # Clear any existing handlers to avoid duplicates on re-initialization
-    root_logger.handlers.clear()
-
-    root_logger.setLevel(level)
-
-    # Console handler
-    if console:
-        console_handler = logging.StreamHandler(sys.stdout)
-        console_handler.setLevel(level)
-
-        if simple_console:
-            console_format = logging.Formatter(SIMPLE_FORMAT)
-        else:
-            console_format = logging.Formatter(DEFAULT_FORMAT, datefmt=DEFAULT_DATE_FORMAT)
-
-        console_handler.setFormatter(console_format)
-        root_logger.addHandler(console_handler)
-
-    # File handler
-    if file_logging:
-        if log_dir is None:
-            log_dir = Path("./logs")
-
-        log_dir.mkdir(parents=True, exist_ok=True)
-
-        log_filename = f"pathways_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
-        log_path = log_dir / log_filename
-
-        file_handler = logging.FileHandler(log_path, encoding="utf-8")
-        file_handler.setLevel(level)
-        file_handler.setFormatter(
-            logging.Formatter(DEFAULT_FORMAT, datefmt=DEFAULT_DATE_FORMAT)
-        )
-        root_logger.addHandler(file_handler)
-
-    return root_logger
-
-
-def get_logger(name: str) -> logging.Logger:
-    """
-    Get a logger for a specific module.
-
-    Args:
-        name: Module name (typically __name__)
-
-    Returns:
-        Logger instance configured as child of root pathways logger
-
-    Usage:
-        from core.logging_config import get_logger
-        logger = get_logger(__name__)
-        logger.info("Processing started")
-        logger.error("Something went wrong")
-    """
-    # Create child logger under the pathways namespace
-    if name.startswith("pathways."):
-        return logging.getLogger(name)
-    return logging.getLogger(f"pathways.{name}")
-
-
-# Module-level loggers for common components
-data_logger = get_logger("data")
-dashboard_logger = get_logger("dashboard")
-gui_logger = get_logger("gui")