Fix evolution run skills root alignment

[cursor]

Summary

• Fixes a high-severity evolution path split where skilllite evolution run wrote generated pending skills under workspace/.skills, while desktop pending/status/confirm read the effective skills/ root.
• Reuses the existing resolve_skills_dir_with_legacy_fallback policy so workspaces with skills/ get visible/confirmable pending skills and legacy .skills-only workspaces keep working.
• Updates focused regression tests, stale internal comments, EN/ZH pending-empty UI strings, and task evidence.

Task Linkage

• Task ID: TASK-2026-069
• Task folder: tasks/TASK-2026-069-evolution-run-skills-root/

Injected Specs

• spec/architecture-boundaries.md (commands-layer root resolution reused lower-layer helper; no dependency direction change)
• spec/security-nonnegotiables.md (not sandbox/security scoped)
• spec/testing-policy.md (required for code change)
• spec/docs-sync.md (EN/ZH user-facing strings updated)

Validation Evidence

• Commands executed:
  • rustup update stable && rustup default stable (after Cargo 1.83 failed before tests due edition 2024 dependency metadata)
  • cargo fmt --check
  • cargo test -p skilllite-commands --features agent resolve_skills_root
  • cargo test -p skilllite-commands --features agent
  • cargo test -p skilllite
  • cargo clippy --all-targets -- -D warnings
  • cargo test
  • python3 scripts/validate_tasks.py
• Key results:
  • Focused regressions: 2 passed; 0 failed
  • skilllite-commands: 41 passed; 0 failed
  • skilllite: integration/unit tests passed, including skill management and E2E minimal tests
  • Full workspace cargo test: passed
  • Task validation: Task validation passed (69 task directories checked).

Regression Scope

• Areas likely affected:
  • skilllite evolution run
  • Desktop evolution manual trigger and post-authorize background run
  • Pending evolved skill visibility and confirmation
• Explicit non-goals:
  • DB workspace default semantics when --workspace is omitted
  • Assistant background authorize process/env propagation beyond the skills-root alignment

Docs Sync (EN/ZH)

• Not needed
• Updated EN + ZH docs
• Files:
  • crates/skilllite-assistant/src/i18n/messages/en.ts
  • crates/skilllite-assistant/src/i18n/messages/zh.ts

Review Checklist

• Acceptance criteria in tasks/TASK-2026-069-evolution-run-skills-root/TASK.md satisfied
• tasks/TASK-2026-069-evolution-run-skills-root/STATUS.md updated with latest progress
• tasks/TASK-2026-069-evolution-run-skills-root/REVIEW.md includes merge readiness decision
• tasks/board.md status is up to date