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There is a trade-off between convenience and level of control: currently every providing concept is enabled implicitly, i.e. when its available in the rules, locally or from a plugin. So there's no need to explicit adding them to groups but they might be enabled unintentionally and create an unwanted situation.
My current thoughts are as follows:
providing concepts which are available locally (i.e. in the rules folder jqassistant) should be activated by default, the concepts are here by intention
provding concepts which are available from plugins should be enabled exclicitly, e.g. by adding them to a group
there should be an activation policy for providing concepts (as attribute activation on providesConcept) to control this behavior, e.g. with the following strategies:
local, plugin: as described
always: the concept should be activated whenever it is available, this makes sense e.g. for concepts providing java:GeneratedType
explict: the concept must be activated explicitly, e.g. by adding it to a group
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