Move config module to be instance based and merge bootstrap into config.

helps with #827, otherwise no issue

- This is general code clean-up and unification.
- Merges code from bootstrap.js into config module as they were both
concerned with managing the config file and as such should be in one
location.
- Updates all relevant tests.
Merge pull request #3866 from hswolff/config-updates

Move config module to be instance based and merge bootstrap into config.