Deprecate composition overrides in favor of direct CIF specification

[laubachb]

Summary

Deprecates the transition_metal and group_iv composition override fields in IntermetallicConfig. Users should now specify the starting material directly via the CIF file, with automatic validation that f-block elements are compatible with the search mode.

Motivation

The previous approach of using a template CIF + composition overrides was confusing and not future-proof for:

• Structures with vacancies or partial occupancies
• Doped materials
• Complex starting compositions beyond simple element substitution

Direct CIF specification makes the starting material explicit and enables more sophisticated structure definitions.

Changes

1. Config Validation (core/config.py)

• Deprecation warnings: transition_metal/group_iv fields now emit DeprecationWarning
• F-block validation (when overrides NOT used):
  • f_block_mode='u_only': requires U (atomic 92) in CIF
  • f_block_mode='lanthanides_u' or 'lanthanides_u_no_wrap': requires lanthanides (57-71) or U (92)
  • f_block_mode='full_f_block': accepts all f-block elements
  • Warns if no f-block elements found (allows for testing)

2. Builder Documentation (cli/builders.py)

• Added deprecation comment above composition override logic
• Logic unchanged for backward compatibility

3. Documentation

• Created REFACTOR_NOTES.md with full migration guide
• Added examples/config_intermetallic_new_style.yaml showing new approach

Backward Compatibility

All existing configs continue to work (with deprecation warnings)

• The 18 sensitivity study configs using overrides are unaffected
• Override mechanism in builders.py remains functional
• Validation skipped when overrides are present

Migration Example

Before (deprecated):

intermetallic:
  structure_path: mat_Pb6U1W6_sg191.cif  # Template
  transition_metal: Cr
  group_iv: Sn
  f_block_mode: u_only