filsystem MCP default args is appended instead of replaced

[reegnz]

Bug description

The filesystem MCP config in the registry is misbehaving, and the default args cannot be overridden properly.

Steps to reproduce

thv run --volume /Users/$USER/repos/github.com/stacklok/toolhive:/Users/$USER/repos/github.com/stacklok/toolhive filesystem -- /Users/$USER/repos/github.com/stacklok/toolhive

After launching I'm seeing this error:

❯ thv logs filesystem
Error accessing directory /projects: Error: ENOENT: no such file or directory, stat '/projects'
    at async Object.stat (node:internal/fs/promises:1031:18)
    at async file:///app/dist/index.js:33:23
    at async Promise.all (index 1)
    at async file:///app/dist/index.js:31:1 {
  errno: -2,
  code: 'ENOENT',
  syscall: 'stat',
  path: '/projects'
}

The docker image launched by the thv cli seems to append the default /projects to the args, even if there's user-provided args:

❯ docker inspect filesystem  | jq '.[].Args'
[
  "/app/dist/index.js",
  "/Users/zoltanreegn/reegnz/github.com/stacklok/toolhive",
  "/projects"
]

Expected behavior

When providing cli args to the thv run command they override the default args.

Actual behavior

The default args are not overridden, they are appended to the user-provided arg list.
The docker container spawned by the command appends /projects to the provided list of args, making it /home/user/mydir /projects.

Environment (if relevant)

• OS/version: macOS 15.5
• ToolHive version: v0.2.0

Additional context

Seems like #1118 introduced this issue.

[reegnz]

For the record, I am aware of the workaround to not provide args and mount under /projects.
But this has the disadvantage that the file path in the MCP will be different from the file path found in the IDE using the MCP.
Another workaround is to just mount /dev/null to /projects/null.

Ideally defaults should be defaults, which can be fully overridden, not appended to the existing args.