fix: merge system and user settings data

[hileix]

Summary

• split settings storage into system defaults and user/worktree overrides
• merge workflows, AI API profiles, managed skills, and work folders for Settings
• keep deletes as user-layer tombstones so system defaults are not mutated
• remove legacy/fallback migration behavior for old settings locations

Verification

• pnpm --dir apps/desktop/renderer test src/lib/ai-api-config.test.ts src/lib/workflow-dsl.test.ts src/lib/worktree-config.test.ts src/lib/skills-storage.test.ts src/lib/workfolders-storage.test.ts src/lib/workflow-storage.test.ts --run
• pnpm build:desktop
• git diff --check