Fix evolution workspace run scoping

[cursor]

Summary

• Fixes a critical workspace split where desktop chat/evolution run paths could write decisions, authorized proposals, or generated pending skills outside the workspace the UI reads.
• Uses existing workspace and skills/.skills fallback helpers instead of adding new storage semantics.

Task Linkage

• Task ID: TASK-2026-069
• Task folder: tasks/TASK-2026-069-evolution-workspace-run-scope/

Injected Specs

• spec/architecture-boundaries.md (assistant/CLI/agent boundary touched without dependency direction changes)
• spec/security-nonnegotiables.md (not sandbox/security policy)
• spec/testing-policy.md (Rust code change)
• spec/docs-sync.md (reviewed; no docs needed because this restores intended behavior without new flags/env surface)

Validation Evidence

• Commands executed:
  • cargo fmt --check
  • cargo test -p skilllite-commands --features agent
  • cargo test -p skilllite-agent
  • cargo test --manifest-path crates/skilllite-assistant/src-tauri/Cargo.toml
  • cargo test -p skilllite
  • cargo clippy --all-targets -- -D warnings
  • cargo clippy --manifest-path crates/skilllite-assistant/src-tauri/Cargo.toml --all-targets -- -D warnings
  • cargo test
  • python3 scripts/validate_tasks.py
• Key results:
  • Main workspace fmt, clippy, focused tests, cargo test -p skilllite, and full cargo test passed.
  • Assistant Tauri tests passed: 53 passed; 0 failed after installing Linux Tauri deps and building frontend dist.
  • Assistant standalone clippy with -D warnings is blocked by existing unrelated lint baseline (unused_imports, dead_code, clippy::unnecessary_sort_by), recorded in REVIEW.md.
  • Task validation passed: 69 task directories checked.

Regression Scope

• Areas likely affected:
  • skilllite evolution run
  • Desktop agent-rpc chat subprocess environment
  • Agent in-process A9 evolution
  • Desktop authorize-capability follow-up run
  • Life Pulse automatic growth run
  • Pending evolved skill list/confirm/reject
• Explicit non-goals:
  • evolution reset/disable/explain workspace semantics
  • Broader force/manual governance policy changes
  • LLM provider settings UX changes

Docs Sync (EN/ZH)

• Not needed
• Updated EN + ZH docs
• Files:
  • N/A

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