Keep $ref dereference when writing the update files

Currently, openapi-format dereferences the OpenAPI documents to do its formatting, sorting, ... and write a dereferenced result.

Investigate the option to leverage: https://www.npmjs.com/package/json-refs to format the OpenAPI documents and update the $ref values in different files.

const jsonRefs = require('json-refs');

const json = {
  "foo": {
    "$ref": "#/bar"
  },
  "bar": {
    "baz": "qux"
  }
};

const options = {
  filter: ['relative', 'remote'],
  loaderOptions: {
    processContent: (res, callback) => callback(undefined, res.text)
  }
};

jsonRefs.resolveRefs(json, options).then(
  (results) => {
    // make changes to the resolved object
    results.resolved.bar.baz = "newValue";
    // write the changes to the $ref locations
    jsonRefs.updateRefs(results.refs, results.resolved).then(
      (updated) => console.log(updated),
      (err) => console.log(err)
    );
  },
  (err) => console.log(err)
);

Start by reviewing openapi-format's current dereference, formatting, and file-writing flow, then read the linked json-refs example for resolveRefs and updateRefs. Done should mean formatted OpenAPI documents preserve their $ref values and propagate changes back to the referenced files.