Repair Vault and app startup no longer create or recreate the _themes/
directory (legacy JSON theme store). All config files — theme notes,
theme.md, config.md, AGENTS.md — are seeded exclusively at vault root.
- Remove seed_default_themes() and all _themes/ creation paths
- Add migrate_legacy_themes_dir() to clean up _themes/ with only defaults
- Stop list_themes() from auto-creating _themes/ when absent
- Remove _themes from KEEP_FOLDERS and PROTECTED_FOLDERS (flatten-safe)
- Fix create_theme() to error instead of recreating _themes/
- Remove _themes/ seeding from create_getting_started_vault()
- Update all affected tests (642 Rust + 2253 frontend pass)
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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