There is a framework called Grails.
Is that sentence correct?
The Grails have integration with jUnit
Don't let the final 's' fool you, Grails is singular. So:
Actually, both answers can be correct.
Grails have been used for many centuries.
Grails has been used in many projects.
These are both correct usages. However, the further clarification you gave in your quoted text showed that you were referring to the software implementation "Grails". In this case, the proper name of the product is "Grails". The "s" at the end is not indicating a plural, it's just part of the name.
The confusion comes in because it's not common to have singular English nouns end in "s".
Look at it this way. If you use the proper name "Leonides" as your example:
Leonides has given the order to attack".
If, on the other hand, there was a small, furry creature called a "leonide", you would say:
Leonides have been known to attack without provocation.
Hopefully this helps.