apollo.config.js is overriden by default flags

[klujanrosas]

While trying out the new apollo.config.js file, I couldn't manage to get past the following error:

I dived into the source and discovered that the oclif.manifest.json defines a default queries value

{
  "queries":{
    "name": "queries",
    "type": "option",
    "description": "Path to your GraphQL queries, can include search tokens like **",
    "default":"**/*.graphql"
  }
}

That wouldn't be a problem until I spotted a suspicious check being performed here:
https://github.com/apollographql/apollo-cli/blob/8d8221da4b6aa775a4046b0661647eee4d388d60/packages/apollo-cli/src/load-config.ts#L62-L70

Which basically is overriding the values specified in apollo.config.js, since flags.queries always holds a value.

I'll get my hands on this and submit a PR if you agree!
I couldn't help myself and went ahead and submitted a PR

Thank you for making this awesome tool!