refactor: migrate runtime thread state into sessions storage

[LIU9293]

Summary

• move thread activity tracking and pending restart message persistence from settings.json to ~/.config/ode/sessions
• expose session-centric helpers directly from packages/config/local/sessions.ts and update all runtime/agent imports to use them
• remove the legacy packages/config/local/settings.ts flow and stop re-exporting it from packages/config/local/index.ts

Validation

• bun install
• bun test packages/core/test/message-dedup.test.ts packages/core/test/session-retention.test.ts packages/core/test/recovery.test.ts
• bun test packages/ims/shared/incoming-message-processor.test.ts
• bun test packages/agents/test/cli-command.test.ts
• bun test packages/ims/slack/message-router.test.ts