Npm prune and the removal of a file: dependency

I have a local npm package (node.js add-on) that we install via the file.

npm i --save my_package-1.0.0-beta.1.tgz

The package.json file lands up looking like this

{
  ...
  "dependencies": {
    "my_package": "file:my_package-1.0.0-beta.1.tgz",
    ...
  },
}

The module is used in the code, extensively.

When I run npm prune, the package is removed from node_modules. How can I configure or npm prune to not remove this package?

via Niall