[~TASK] FLOW3 (Configuration): Fix configuration loading
When loading configuration, contexts were not used for all applicable
types, this is done now.
The more important change is the handling of FLOW3 package settings.
Before they were loaded early in the bootstrap and then never again. Now
they are loaded also when other packages's settings are loaded, but
always come first (as the base settings). This allows to have
context-specific settings from FLOW3 to "survive" general settings from