customize-schemas.php is not idempotent

[dpash]

Running customize-schemas.php multiple times results in further modifications of the schemas.

There's three issues:

1. Security information is stripped away, as it doesn't take existing data into account.
2. 'x-expose-headers' is added where as previously it's not included. This seems to be a bug due to it being stripped out when first run.
3. Additions are added multiple times (which results in invalid json due to duplicate parameters in orders.json)

I have fixes for the first two and I'll create a PR for these. I still need to figure out how to resolve the addition issue.

An alternative approach is to download the original schemas to a different directory and then have the customize-schemas.php write out the schemas to new files.