chore: align with current standards and upgrade dependencies

[lpatiny]

Summary

• Align tooling with the cheminfo generator (scripts, dependency ordering, tsconfig types, .npmrc ignore-scripts)
• Upgrade dependencies to latest (ESLint kept on 9.x; TypeScript on 6.x; ml-gsd 13 → 14)
• Use the istanbul coverage provider (numeric package) and add snapshotFormat.maxOutputLength
• Add .claude to .gitignore

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.09%. Comparing base (5838943) to head (99f34cb).

❗ There is a different number of reports uploaded between BASE (5838943) and HEAD (99f34cb). Click for more details.

HEAD has 1 upload less than BASE

Flag	BASE (5838943)	HEAD (99f34cb)
	4	3

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #35      +/-   ##
==========================================
- Coverage   93.37%   86.09%   -7.29%     
==========================================
  Files          33       33              
  Lines         151      151              
  Branches       34       34              
==========================================
- Hits          141      130      -11     
- Misses         10       21      +11     

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