Include subpackage checking

[CatarinaGamboa]

Previously we were not checking for subpackages for refinements.
Somehow it works in the extension (@rcosta358 maybe you did some trick?) but using the verifier alone we were erasing the information from the parent package refinements and not checking the insides.
For example:

| FileRefinements.java
| TestIncorrect.java // would be caught as an error
| test
 -| TestIncorrect2.java // would not be checked with the info from FileRefinements

This PR fixes that

[CatarinaGamboa]

@rcosta358 check if this doesnt break anything from the extension side pls

[rcosta358]

lgtm. also tested in the extension.