fix: prevent sqlite reimport over legacy vault

[antonreshetov]

Summary

• prevent auto-migration from sqlite when the markdown vault already contains legacy-root data
• reuse markdown runtime path resolution so startup detects migrated legacy vaults before deciding to import
• add a regression test covering the legacy markdown-vault layout from issue [Bug]: Upgrading to 5.0 will re-run sqlite import even if previously imported, deleting all existing data #727

Test Plan

• pnpm test src/main/storage/providers/markdown/runtime/tests/paths.test.ts
• pnpm exec eslint src/main/index.ts src/main/storage/providers/markdown/index.ts src/main/storage/providers/markdown/runtime/index.ts src/main/storage/providers/markdown/runtime/paths.ts src/main/storage/providers/markdown/runtime/tests/paths.test.ts

Closes #727