add JSON Schema to validate user input files before initialization.

[janitha-mahanthe]

Feature: Add JSON Schema for Input Validation

• Required top-level keys (simulation_name, replicas, monomers)
• Conditional requirements:
  • method: "ratio" → require monomer_ratios
  • method: "counts" → require monomer_counts
• Monomer name uniqueness
• Systems must reference only defined monomer names
• Fail fast with clear validation errors

Impact
Improves robustness, user experience, and maintainability of the v0.2 class-based refactor.