Use JSON for the database instead of YAML. (#2189)

* Use JSON for the database instead of YAML.

- JSON is much faster than YAML *and* can preserve ordered keys.
  - 170x+ faster than Python YAML when using unordered dicts
  - 55x faster than Python YAML (both using OrderedDicts)
  - 8x faster than C YAML (with OrderedDicts)

- JSON is built into Python, unlike C YAML, so doesn't add a dependency.
- Don't need human readability for the package database.
- JSON requires no major changes to the code -- same object model as YAML.
- add to_json, from_json methods to spec.

* Add tests to ensure JSON and YAML don't need to be ordered in DB.

* Write index.json first time it's not found instead of requiring reindex.

* flake8 bug.

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