De-couple XML from tool interface for test collections.

[jmchilton]

Keep more in JSON longer so we can apply less custom model objects for validation and stuff. The interface is returning more pure json now.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.