upgrader: change to module-aware engine

• Changes upgrader to load upgrades from all installed modules.

• Changes upgrade naming convention to be compatible with invenio modules.

• Changes upgrader to use SQLAlchemy models for querying instead of run_sql.

• Changes recipe creation to use module import paths as input instead of system paths.

• Relaxes constraint on cross-graph dependencies to allow inter-module dependencies.

• Removes pre-upgrade check for legacy custom templates.

• Adds tests of recipe creation.

• Fixes PEP8 issues.

Signed-off-by: Lars Holm Nielsen <lars.holm.nielsen@cern.ch>