feat: split --vacancy into --vacancy-index and --vacancy-count

[ToAmano]

Refactors vacancy creation options in the CLI and core to address Issue #26.

Closes #26

1. Splits the old heuristic-based --vacancy option into two unambiguous options:
   • --vacancy-index: For removing atoms at specific absolute indices (e.g. Si:0, C:33).
   • --vacancy-count: For randomly removing a specified number of atoms of an element.
2. Maintains backward compatibility by aliasing --vacancy to --vacancy-index.
3. Replaces the 3C-SiC vacancy example in examples/4_espresso_supercell to demonstrate a double vacancy creation (removing Si:0 and C:33) via the command line.
4. Adds comprehensive unit and integration tests for both index-based and count-based vacancy generation.
5. Updates README.md documentation and examples.

[cr-gpt]

Seems you are using me but didn't get OPENAI_API_KEY seted in Variables/Secrets for this repo. you could follow readme for more information

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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