Add comprehensive GaMD stage configuration validation

[alex-sbaq]

Add comprehensive stage configuration validation

Problem

Users were experiencing confusing errors when stage configurations were invalid:

• Overlapping stage boundaries causing simulation failures
• Cumulative vs individual stage parameter confusion
• Poor error messages making debugging difficult

Solution

Added comprehensive validation in gamd/stage_integrator.py:

• Stage boundary validation: Ensures no overlaps between stages
• Parameter validation: Validates all stage-specific parameters
• Clear error messages: Detailed explanations of configuration problems
• Early failure: Catches errors during initialization, not runtime

Features

• Validates all 5 stages: equilibration, restraint, conventional MD, acceleration, production
• Checks for cumulative parameter consistency
• Provides specific suggestions for fixing configuration issues
• Maintains backward compatibility with existing configurations

Technical Implementation

• New _validate_stage_configuration() method in StageIntegrator
• Comprehensive boundary checking logic
• User-friendly error messages with context
• Called during integrator initialization

Testing

• All existing tests pass
• Validation catches configuration errors early
• Clear error messages help users debug issues quickly

Impact

• User Experience: Much clearer error messages for configuration issues
• Reliability: Prevents runtime failures from invalid configurations
• Maintainability: Easier to debug user configuration problems