Hi Flavia,
AbstractFungalRADeployer is the correct place to put your changes, just don't change validation issue, because it's not matter of validation but how deployers would accept deployments.
Regarding directory, it's ok since IJ has a bit more abstraction in deployers and it's up to subclasses of this AbstractFungalRADeployer refine their accepts() method.
I'm hoping this would answer your questions, otherwise feel free to ask.
regards
S.