docs: add calculation examples

[tdpham2]

Summary

MatKit's calculation workflows lacked a consolidated set of runnable examples using public APIs. Add four Python programs and a Python/CLI guide covering Zeo++ analysis and screening, single-component gRASPA execution and pressure sweeps, mixture preparation, and MLIP evaluation, fixed-cell relaxation, and batches across MACE, Rootstock, and ALCHEMI.

The examples delegate engine execution, parsing, and persistence to MatKit. Add 20 example tests and include the new programs and tests in CI lint checks. No files under src/ change.

Validation

• PYTHONPATH=src python -m pytest -q --ignore=tests/test_mcp_api.py: 405 passed, 1 skipped, including 20 new example tests.
• Ruff lint and formatting checks passed for src/, the new programs, and their tests; the new files are included in CI lint checks.
• Guide JSON specifications validate against the public request/profile models; Python snippets and local links were checked.
• git diff --check passed.

The local MCP tests were excluded because the installed SDK is 1.16.0 while the project requires SDK 2. Tests use synthetic engines and calculator doubles; no real-engine or GPU execution was available. Mixture examples prepare inputs only, matching the current public API capability.