docs: prepare v0.2.4 for pyOpenSci readiness

[NanoBiostructuresRG]

Summary

This PR prepares HARMONSMILE dev/v0.2.4 for pyOpenSci-oriented review readiness.

Main changes:

• Strengthens project documentation for external scientific users.
• Adds and refines contribution and code-of-conduct guidance.
• Aligns citation metadata and DOI references for v0.2.4.
• Improves MkDocs layout responsiveness and prevents table overflow.
• Adds a dedicated Usage page and keeps the Home page focused on scientific motivation, workflow overview, and navigation.
• Ensures MkDocs build output is ignored via .gitignore.

Validation

• git diff --check
• python -m mkdocs build --strict
• Local visual inspection of:
  • /harmonsmile/
  • /harmonsmile/usage/
  • /harmonsmile/api/
  • /harmonsmile/changelog/

No package source code, API behavior, CLI behavior, chemistry behavior, or workflow behavior was changed.