MCP `npx` and `uvx` based extensions still broken

[SalvatoreT]

Describe the bug

npx and uvx based extensions are unusable after @Kvadratni's change (#3148) to address the npx missing issue (#3139).

To Reproduce
Steps to reproduce the behavior:

1. On main run the just run-ui command.
2. Add the Knowledge Graph Settings extension (or any MCP extension)

   npx -y @modelcontextprotocol/server-memory
   

3. Observe the error

Expected behavior
The extensions should start.

Screenshots

Please provide following information:

• OS & Arch: macOS, ARM64
• Interface: UI
• Version: main, v1.0.30, fdafbca92e88697aadb7deaa7b746a0f8ac13c41
• Extensions enabled: Computer Controller, Developer, Memory
• Provider & Model: Google - gemini-2.5-pro-preview-06-05

Additional context

Here's the error message.

Error activating extension: Failed to add extension configuration, error: Transport(StdioProcessError("Permission denied (os error 13)"))

[SalvatoreT]

If you look at the permissions, the npx, uvx, and jbang are different.

❯ ls -al ui/desktop/src/bin
total 659320
drwxr-xr-x@  9 sal  staff        288 Jun 29 22:50 .
drwxr-xr-x@ 34 sal  staff       1088 Jun 29 22:50 ..
-rw-r--r--@  1 sal  staff          0 Feb 23 23:45 .gitkeep
-rwxr-xr-x@  1 sal  staff  159786000 Jun 29 22:44 goose
-rwxr-xr-x@  1 sal  staff  150085824 Jun 29 22:44 goosed
-rw-r--r--@  1 sal  staff       3300 Jun 29 22:50 jbang
-rw-r--r--@  1 sal  staff          0 Jun 29 22:50 npx
-rwxr-xr-x@  1 sal  staff   27687586 Jun 29 22:42 temporal-service
-rw-r--r--@  1 sal  staff          0 Jun 29 22:50 uvx

[SalvatoreT]

After I fix the permissions...

chmod +x ui/desktop/src/bin/{npx,uvx,jbang}

... and restart Goose, I still have errors.

Error activating extension: Failed to add extension configuration, error: Initialization(Stdio { name: "knowledgegraphmemory", cmd: "/Users/sal/Developer/goose/ui/desktop/src/bin/npx", args: ["-y", "@modelcontextprotocol/server-memory"], envs: Envs { map: {} }, env_keys: [], timeout: Some(300), description: None, bundled: None }, McpServerError { method: "initialize", server: "", source: ServerBoxError(StdioProcessError("Process ended unexpectedly")) })

[SalvatoreT]

Okay, I figured out the issue. It stems from this little snippet where we're swapping out the cmd path. cc @Kvadratni

goose/ui/desktop/src/components/settings/extensions/agent-api.ts

Lines 146 to 148 in a89fa18

	if (extension.type === 'stdio') {
	extension.cmd = await replaceWithShims(extension.cmd);
	}

When I go to add/enable an extension, the cmd path is interpolated to use the Desktop UI's binaries. When I comment that out, the cmd doesn't point to the absolute path.

14:47:19.722 › goosed stdout for port 61767 and dir /Users/sal/Developer/goose:   2025-06-30T12:47:19.722537Z  INFO goosed::routes::extension: Received extension request: {
   "args": [
     "-y",
     "@modelcontextprotocol/server-memory"
   ],
   "bundled": null,
-  "cmd": "/Users/sal/Developer/goose/ui/desktop/src/bin/npx",
+  "cmd": "npx",
   "description": "Graph-based memory system for persistent knowledge storage",
   "enabled": false,
   "env_keys": [],
   "envs": {},
   "name": "knowledgegraphmemory",
   "timeout": 300,
   "type": "stdio"
 }
     at crates/goose-server/src/routes/extension.rs:90

[SalvatoreT]

I'll open a PR with this fix.

[SalvatoreT]

Another option would be for replaceWithShims to point to whichever folder the Goose server uses.

[Kvadratni]

dammit I though I fixed this one. Thanks for looking into it

[Kvadratni]

I don't think that's the culprit. This shim script has been there for 2 months and we definitely need it

[Kvadratni]

merged the chmod fix. Will build from source again and test
#3169

[Kvadratni]

Ok I found the issue. fixing now.

[Kvadratni]

I was a bit hasty and didn't notice that I merged the binaries empty
#3170
thsi should fix it

[ahau-square]

we released a new version tonight, let me know if you're still having issues @SalvatoreT !