Introduce new method to mark a repository processed.

Unsure why Repository instances were needed for this,
but as request deal with repository IDs (and the getter
gives unmodifiable list), currently it's impossible to
"pass over" cycle detection context from one request
to it's offspring.

Needed for NXCM-4752
NEXUS-4207: Default value for Publish URL combo
[NXCM-2985] Log server form validation (ConfigurationException) at debug level (instead of warn), as there is nothing to be worried about :D

Signed-off-by: Alin Dreghiciu <adreghiciu@gmail.com>
Disallow Maven 3.1 this is not yet supported due to aether change.
Merge remote-tracking branch 'origin/master' into edit-js-in-place-poc