sdk.prompt({ tools }) does not override agent configured permissions

[jquense]

Description

When using the SDK, session.prompt({ tools: { question: true } }) does not expose the tool to the model if the selected agent has permission: {}. I believe this is true for any permission that is denied by the agent

Plugins

none

OpenCode version

1.2.24

Steps to reproduce

1. Configure an agent like this:

{
  "agent": {
    "repro": {
      "mode": "primary",
      "model": "anthropic/claude-sonnet-4-5-20250929",
      "permission": {}
    }
  }
}

2. Create a session through the SDK
3. Call session.prompt() with:

{
  sessionID,
  agent: "repro",
  tools: { question: true },
  parts: [
    { type: "text", text: "do you have a question tool?" }
  ]
}

4. Observe the model response