fix: use shared settings directory for all instances

[hileix]

Summary

• Make all desktop instances read and write the same shared app settings directory
• Remove development worktree-scoped settings path logic
• Remove system/user config merge behavior and write the full config directly
• Update storage tests to match the single shared directory model

Verification

• pnpm --dir apps/desktop/renderer test --run
• pnpm build:desktop
• Confirmed CONFIG_FILE and SYSTEM_CONFIG_FILE both resolve to /Users/mac/Library/Application Support/dev-Workflow/config.json
• API smoke test: /api/settings/ai-api-profiles reads the shared config file