build(deps): bump jsondiffpatch and agents in /doit-mcp-server

Removes [jsondiffpatch](https://github.com/benjamine/jsondiffpatch). It's no longer used after updating ancestor dependency [agents](https://github.com/cloudflare/agents/tree/HEAD/packages/agents). These dependencies need to be updated together.


Removes `jsondiffpatch`

Updates `agents` from 0.0.95 to 0.1.3
- [Release notes](https://github.com/cloudflare/agents/releases)
- [Changelog](https://github.com/cloudflare/agents/blob/main/packages/agents/CHANGELOG.md)
- [Commits](https://github.com/cloudflare/agents/commits/[email protected]/packages/agents)

---
updated-dependencies:
- dependency-name: jsondiffpatch
  dependency-version: 
  dependency-type: indirect
- dependency-name: agents
  dependency-version: 0.1.3
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

Author: dependabot[bot]