Removed deleted elements.

refs #16053
Merge branch 'enhancement/16053' into develop
config: moving to a folder structure

allowing for multiple configs

refs #16017
config: cleanup the default dist

refs #16017
ignore: new configs

refs #16017
app_factory: now using an app factory

refs #16017
manage: initdb works with the app factory

refs #16017
removed run.py

refs #16017
README: updated to reflect run.py change

refs #16017
app factory: use the current app instead of creating new ones

refs #16017
util: add missing import

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api: added missing import

refs #16017
category: corrected mispelling

refs #16017
util: added before_request method to setup a db session

refs #16017
api,util: use g.db_session

refs #16017