docs: replace three dead documentation links (sympy, bids, molecular-dynamics)

[rudycelekli]

Problem

Three "Additional Resources" links in SKILL.md files return HTTP 404, so agents following them get nothing.

Evidence

I extracted every unique URL from skills//SKILL.md, README.md, CONTRIBUTING.md, AGENTS.md and docs/.md (956) and requested each one. Documentation links that 404 (confirmed with a browser User-Agent and GET):

• skills/sympy/SKILL.md: https://github.com/sympy/sympy/tree/master/examples (the examples/ directory no longer exists at the repo root)
• skills/bids/SKILL.md: https://bids-standard.github.io/bids-starter-kit/ (the starter kit moved into the BIDS website)
• skills/molecular-dynamics/SKILL.md: https://openmm.org/documentation.html

Change

One line each, pointing to live equivalents (all return 200):

• sympy: https://docs.sympy.org/latest/guides/index.html
• bids: https://bids-website.readthedocs.io/en/latest/getting_started/index.html
• openmm: https://docs.openmm.org/

Frontmatter is untouched. I did not touch API endpoints that return 401/405/406 to unauthenticated requests, since those are expected.

How verified

curl on each old URL (404) and new URL (200). Also checked that name/description frontmatter of all 177 skills already satisfies the spec limits (name matches directory, description at most 1024 characters) and that the README/docs skill counts (177) match skills/, so nothing else needed changing there.

🤖 Generated with Claude Code