At the top of the pack file there are a couple of rules you can set up to change the behavior. Again thanks to neofuturelabs for sharing this info.
The settings I ended up with for the header are are as follows
Below that you can then specify a list of folders and files which you want to exclude from your package.
A file can be excluded as follows and the .* at the end means that all file types with this name will be excluded. Often there is a set of a .uexp and .uheader file and we need to exclude both to not have any remaining dependencies**.**
+Files=".../Engine/Content/EditorMaterials/MatineeGroups/MAT_Groups_Director.*"
To exclude a folder you want to write the folder name and at the end put a /* to exclude everything within that folder including subfolders.
+Files=".../Engine/Content/Maps/*"
In my case however this actually did not work and I had to remove the * at the end to sucessfully exclude an entire folder.
+Files=".../Engine/Content/Maps/*"
I will give you my recommendations of files that I believe are safe to exclude under certain circumstances, but I will also teach you how you can unpack the .pak and .ucas file to look through all of the files and decide by yourself what isn’t necessary.