Dependency refresh and documentation alignment.

Updated:
- @cyanheads/mcp-ts-core ^0.3.5 -> ^0.3.7
- fast-xml-parser ^5.5.12 -> ^5.7.1
- sanitize-html ^2.17.2 -> ^2.17.3
- @biomejs/biome ^2.4.11 -> ^2.4.12
- typescript ^6.0.2 -> ^6.0.3

Removed:
- package.json overrides block (9 transitive pins). All have shipped
  patched versions upstream; bun audit remains clean without them.

Refactored:
- Collapsed multi-line + string concatenation in pubmed_search_articles,
  pubmed_fetch_fulltext, and pubmed_convert_ids descriptions to single
  strings, aligning with the project convention and updated skill guidance.

Docs:
- Synced add-tool (v1.4) and design-mcp-server (v2.3) skills from the
  framework; both now emphasize single-paragraph tool descriptions.