Add v2 logs, network config, and file operations to public API spec (#172)

* Include v2 logs endpoint, network config, and file operations in public API spec

* Add v2 logs endpoint summary and restore deprecation notice on v1

- Add sidebar summary for /v2/sandboxes/{sandboxID}/logs matching other v2 endpoints
- Restore deprecation description on v1 logs endpoint pointing to v2
- Remove outdated phantom deprecation fix from generate script

Author: beran-t