docs: fix outdated links and incorrect repository references

- Update schema links in README.md from 2025-11-25 to 2026-07-28
- Fix grammar in AGENTS.md (aspect -> aspects, remove extra comma)
- Fix bugs URL in package.json (specification -> modelcontextprotocol)
- Fix description in tools/sep-automation/package.json

Signed-off-by: dongjiang <dongjiang1989@126.com>