chore(issues): update follow-up issues after kit-based domain filtering

[JustAGhosT]

Summary

• Marks 006 (CLI-spec parity) as Resolved — framework command types and Phase 10 parity check merged via PR feat(engine): kit-based domain selection, init wizard, stop hook perf #432
• Marks 040 (elegance-guidelines) as Resolved — elegance-guidelines field merged into agents.yaml via PR feat(engine): kit-based domain selection, init wizard, stop hook perf #432
• Marks 025 (TRAE rules) as Partially resolved — filterDomainsByStack() addresses domain noise; TRAE format audit remains outstanding
• Updates 026 (TRAE skills) as In progress / follow-up needed — same filtering principle applies to skills
• Marks 027 (TRAE agents) as Deferred — TRAE packaging/import format audit not yet started
• Downgrades 004 (rules.yaml ownership) from P2 → P3 — domain filtering reduces governance urgency

Test plan

• grep -r "## Resolution\|## Note\|## Status" .github/ISSUES/*.md confirms all 6 files updated
• CI passes (markdown-only changes, no spec drift)

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