fix(gemini): normalize malformed schema nodes before cleanup

- Added a preprocessing pass to repair malformed MCP-style JSON schemas.
- Wraps bare property maps as object schemas, promotes `required: true` flags to parent `required` arrays, and removes boolean `required` from properties.
- Recurses through nested schema containers and skips known API request envelopes to avoid rewriting non-schema docs.
- Switched schema decoding/serialization path to preserve large numeric values and avoid HTML-escaping side effects.

Closes: #5178