Goose can't write to file or call mcp servers even in autonomous mode

[paoloricciuti]

Describe the bug

We talked already in discord here but the gist of it is that for some reason my goose it's not doing any tool call, and it can't even write to files even if it's in autonomous mode.

To Reproduce
Steps to reproduce the behaviour:

1. Open goose
2. Set autonomous mode
3. Ask to call an MCP server or write a file
4. See how the response is that it needs permissions

(I'm sure this doesn't happen to everybody, but unfortunately I have no idea what settings could have caused this)

Expected behaviour
Goose should be able to call MCP tools or write files in autonomous mode

Screenshots

Please provide following information:

• OS & Arch: MacOS
• Interface: UI
• Version: 1.12.0
• Extensions enabled: Developer, Extension Manager, Todo, Svelte
• Provider & Model: claude-code

Additional context
If it could help, goose was not able to run the claude bin, so I had to set CLAUDE_COMMAND to the actual file /Users/paoloricciuti/.volta/bin/claude. I also had one moment when it was making tool calls but not on the svelte extension. I figured out it was a problem with our MCP server, but now the problem it's there even if the extension is not even installed any more.

[blackgirlbytes]

note to try this with the svelte mcp server if you're looking to reproduce -- https://mcp.svelte.dev/mcp

[paoloricciuti]

note to try this with the svelte mcp server if you're looking to reproduce -- https://mcp.svelte.dev/mcp

Nope, my goose can't call extensions or write to file even if I don't have the svelte extension installed at all

[DOsinga]

can you switch off the svelte extension and see if it works there?

[DOsinga]

I believe this is particular to the svelte tool. We've seen this before where goose thinks it does not have access to the svelte tool and then asks the user permission to use it even in autonomous mode. I wonder if it has to do with the naming here, there's a - in the name and there is some weird renaming in the code base going on

[paoloricciuti]

can you switch off the svelte extension and see if it works there?

I completely removed the extension and it can't call any tool or write files

[DOsinga]

for some reason in that screenshot you are missing the little bug icon that should allow you to produce a diagnostics report. can you shut down goose and restart and see if it shows then? it looks like this:

then reproduce the problem and immediately click that button and upload the report.

[paoloricciuti]

diagnostics_20251028_2.zip

Here's with a session I also reproduced the issue with

[codefromthecrypt]

@alexhancock Is this issue about auto-filtering which is like basically saying that goose cannot intervene in any tool/extension managed by the Claude CLI, and no goose tool can be used by it either?

I've not looked deeply, but I just tried the Claude Code integration today and found it can't access anything, and auth notifications don't propagate back to goose. So it could be really easy to get into a bind thinking something would work when it wouldn't. I may be mistaken on this.

Basically, at first I thought it was pass-through LLM (like convenience one-click api-key for anthropic LLMs via the Claude CLI). However, I think pass-through really means delegate all things and not use any goose tools, which if true could explain glitches like this.

[paoloricciuti]

I think @codefromthecrypt is right...it also happens with gemini btw but switching to an Anthropic api key did the trick

[cbruyndoncx]

That is correct, any CLI Provider like claude code, gemini cli take over completely from goose. So the MCP you want to use, you need to setup in the CLI provider MCP settings. So using the CLI provider is a kind of convenience feature to save costs, but actual mileage varies depending on what you want to do as you can see, it means there is less integration with the goose ecosystem overall. Look at it like a cheaper frontend tunnel.

[paoloricciuti]

So there's no way to fix this? I think Claude allows you to "login with Claude code"

[codefromthecrypt]

I have a significant work in progress local to use claude's not well documented approval mcp hook to dispatch approve/deny to goose UX (even if the tools and rules live in Claude still).

The jist is a bit inverted. Goose Claude provider initializes an ephemeral MCP server that complies with Claude's hooks. It then passes that to the CLI args so that when Claude runs into an approval gate it asks Goose. There are devil in details about blocking event loops etc but anyway thats the flow.

I ran into some holes trying to figure out how to elegantly test this. If I dont have a draft PR by Monday, nag me and I will at least raise an issue with the full design I am tinkering with between other tasks.