The file extensions .p & .d have no real significance to the file-type. For example; .p could stand for player or packed. It's really decided at the programmers discretion and could be changed to .apples if you really wanted to.
With Matrix frameworks you need to edit the unpacked file (usually a .txt).
Here is an example, Edit files unpackedCustomSpawnsList.txt then delete the packedSpawns folder. When you reboot the server all the files should automatically re-pack themselves and it will regenerate a packedSpawns folder.
Look inside the classes to see which files need to be deleted in order for them to be re-packed.








