Add runtime settings persistence updates

[DorianZheng]

Summary

• Add SQLite-backed repositories, migrations, and legacy storage migration for settings, secrets, workflow, and runtime state.
• Add backend and coding-engine settings surfaces, bridge APIs, and tests.
• Update the agent runtime to support backend handoff, credential reloads, runtime source/auth seeding, and related persistence paths.
• Include the full requested dirty worktree, including the embedded pr102-review gitlink and local review notes.

Why

This consolidates durable app state behind typed persistence APIs and makes runtime/backend settings manageable from the desktop app.

Impact

Settings and runtime state now flow through repository-backed desktop APIs. Users get UI for backend and coding-engine configuration, while the runtime can reload model credentials and apply backend settings to active agents.

Root Cause

Runtime settings, provider secrets, workflow state, and agent state were spread across legacy storage paths. That made backend selection, credential reloads, and durable runtime state harder to manage consistently.

Validation

• pnpm run typecheck passed.
• pnpm test failed. Current failures include tests/unit/build/install-guard.test.ts requiring ./install-guard.cjs, better-sqlite3 being compiled for a different Node ABI, and two Telegram setup-session snapshot assertions.
• Attempted pnpm rebuild better-sqlite3; rebuild failed because the local disk is full (ENOSPC, about 148 MiB free).