docs(spec-loop): refresh quality-tooling known gaps

[tomatotomata]

Summary

• replace three stale Known gaps with the validator checks that now close them
• name the capability-taxonomy, modes-consistency, and tool-prerequisites checks
• preserve the spec-loop plan's accurate view of remaining work

Validation

• spec-validator run attempted; it reports existing generated .agents/ path and Windows shell fixture violations unrelated to this edit
• git diff --check
• prek run --all-files not run: prek unavailable in this Windows checkout

Closes #938

Generated-by: Codex