Have command line options take precedence over environment variables

Given the following command:

```bash
npm_config_runtime=electron node-pre-gyp install --runtime=node
```

I would expect that `node-pre-gyp` would install for the `node` runtime, but rather it uses the `electron` runtime.

Our use-case is that we have a `.yarnrc` that defines the environment variable, and were trying to run `node-pre-gyp` as part of a yarn run-script to install a native dependency for node for our CI pipeline for testing. I ended up creating a wrapper script around calling `node-pre-gyp` that deleted the `npm_config_*` environment variables that were overriding the option flags I was trying to use.

Reproduce the shown node-pre-gyp install command with conflicting npm_config_runtime and --runtime values, then trace where command-line options and environment variables are parsed. Done means the explicit --runtime=node value takes precedence over the electron environment setting, with coverage for the conflicting-input case.

Written by the indexing model from the issue text.