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.
Uncapitalise middleware should not affect tokens

no issue

- Whilst testing on next, I noticed trying to signup didn't prepopulate email addresses any more, and this is why
Merge pull request #3887 from ErisDS/oops

Uncapitalise middleware should not affect tokens
Run import run operations in order.

Closes #1977, Refs #3473
- Ensure that import operations are run in sequence.
  Previously the operations were started in order but subsequent
  ops were allowed to begin before the previous finished, which would
  result in out-of-order execution.
- Fix bug in attach() where a model property was being passed in
  instead of a transaction object.  If the call was made when a
  transaction was in process, it could cause bookshelf/knex to
  hang and never finish the transaction.
Merge pull request #3891 from jaswilli/import-tests

Run import run operations in order.
Merge pull request #3866 from hswolff/config-updates

Move config module to be instance based and merge bootstrap into config.
Remove shim files that were created to address #1873.

refs #1873

- Removes all shim files.
Merge pull request #2098 from hswolff/remove-file-shims

Remove shim files that were created to address #1873
Merge remote-tracking branch 'upstream/master'
remove readium theme
update to latest ghost