add copy option to bootstrap
add dependencies to requirements

Tweak bash scripts

Refactoring

use sha384 to check identical content

skip md5 when it is not sended

replace real username with test users in tests

updates of files, notes, permissions and tags should be done through the
dedicated end points

also db initialization has been moved before other imports, so that not
it is possible to load collections in Storages

when project permissions get updated propagate them to sessions and
acquisitions

only collections and projects routes can receive permissions updates

bugfixing
adding root checkbox to debug app

fix avatar handling and create schema
filter permissions for containers in handlers

define is_true and has on base.RequestHandler
fix test_collection.py