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When your agent is code — a framework implementation rather than markdown agent files — Helix applies approved fixes by editing that code and opening a pull request on GitHub, the same as for markdown agents.

Mastra

Agents built on the Mastra framework.

Claude Agent SDK

Agents built on the Claude Agent SDK.

DeepAgents (coming soon)

Agents built with DeepAgents.

Pydantic AI (coming soon)

Agents built with Pydantic AI.

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How a fix lands

The flow mirrors markdown agent targets: Diagnose ranks a remedy, you approve it, Helix prepares the code change on a branch, and it opens a GitHub pull request for you to review and merge. Code changes go through the same approval gate — nothing merges without you. Before you start: the repository has a GitHub remote, and gh auth status succeeds or you can push over SSH. Helix opens the pull request with those credentials. Declare a code target in your config:
.mutagent/config.yaml
The loop is the same whether your agent is markdown or code — Evaluate scores it, Diagnose root-causes it, and Optimize applies the approved fix as a PR. Only the target differs.