refactor: migrate settings source of truth to config.json

[h4yfans]

What

Move portable user preferences from SQLite-only storage to <vault>/.memry/config.json as the source of truth. SQLite becomes a read cache for fast IPC performance.

Why

User preferences stored in SQLite are opaque when copying a vault to a new machine pre-sign-in. Additionally, mergeRemote() wrote to synced_settings key but never propagated to the general key the UI reads — settings from other devices were invisible until app restart.

How

• VaultPreferences Zod schema + readPreferences()/writePreferences() for config.json I/O with deep-partial merge
• SET_GENERAL_SETTINGS / SET_EDITOR_SETTINGS: write config.json first (source of truth), then update SQLite cache. Only portable fields go to config.json; startOnBoot, onboardingCompleted stay SQLite-only
• Vault open flow: migrateSettingsToConfig() — if config.json has preferences, use them; if missing, seed from SQLite (one-time backwards-compatible migration)
• settingsHandler.applyUpsert: after mergeRemote(), propagates merged data to config.json, updates SQLite cache, and broadcasts CHANGED events — fixes the synced_settings→general key gap
• Defensive: propagateMergedSettings and broadcastSettingsChanged gracefully handle missing vault path, database, or BrowserWindow (test environments, edge cases)

Type

• refactor — restructure without behavior change

Test plan

• Unit tests added/updated
• Integration tests added/updated

68 new tests across 5 test files:

• vault-preferences.test.ts (15) — schema validation, read/write, partial merge, corruption recovery
• settings-cache.test.ts (7) — SQLite cache population, migration from SQLite→config.json, machine-local field preservation
• settings-handlers.test.ts (+6 = 29 total) — config.json write-through for portable/local/editor fields
• settings-handler.test.ts (6) — sync merge propagation to config.json + CHANGED broadcast
• apply-item.test.ts (25) — existing integration tests still pass

Checklist

• Self-reviewed the diff
• No hardcoded secrets or credentials
• Files stay under ~500 LOC
• Follows immutable data patterns