Fix evolution pending skills root alignment

[cursor]

Summary

• Fixes a high-impact desktop evolution regression where evolution run wrote pending skills to .skills while desktop pending/status/confirm read the effective skills/ root in default workspaces.
• Reuses the shared resolve_skills_dir_with_legacy_fallback policy so default skills/ workspaces and legacy .skills-only workspaces behave consistently.

Task Linkage

• Task ID: TASK-2026-067
• Task folder: tasks/TASK-2026-067-evolution-skills-root-alignment/

Injected Specs

• spec/architecture-boundaries.md (if architecture/layering changed)
• spec/security-nonnegotiables.md (if sandbox/security changed)
• spec/testing-policy.md (required for any code change)
• spec/docs-sync.md (if behavior/docs/env/commands changed)

Validation Evidence

• Commands executed:
  • rustup update stable && rustup default stable
  • cargo test -p skilllite-commands --features agent resolve_skills_root
  • cargo fmt --check
  • cargo clippy --all-targets -- -D warnings
  • cargo test
  • cargo test -p skilllite
  • python3 scripts/validate_tasks.py
• Key results:
  • Focused regression tests: 2 passed; 0 failed.
  • Full workspace tests and skilllite package tests passed.
  • Task validation passed for 67 task directories.

Regression Scope

• Areas likely affected:
  • skilllite evolution run skill root selection.
  • Desktop evolution pending/status/confirm visibility for generated skills.
  • Legacy .skills fallback behavior.
• Explicit non-goals:
  • Skill identity redesign, duplicate skill handling, desktop error UX, and frontend changes.

Docs Sync (EN/ZH)

• Not needed
• Updated EN + ZH docs
• Files:
  • N/A; fix restores the current documented/default skills/ behavior without changing CLI/API shape.

Review Checklist

• Acceptance criteria in tasks/.../TASK.md satisfied (or explicitly deferred)
• tasks/.../STATUS.md updated with latest progress
• tasks/.../REVIEW.md includes merge readiness decision
• tasks/board.md status is up to date