You don't really interact with the Packages root path location directly---that task is handled by the Admin console exclusively for db integrity purposes.
Packages in SD usually have both the package itself and an associated payload. When you go to delete a package from LANrev, the system will ask you if you'd like to delete both the package and the payload, and I usually say yes to both to avoid leaving any orphaned payloads behind.
If you already have a large number of orphaned payloads in that location, you should be able to view them in the payloads sub-directory in the Server Center. You should be able to safely delete them from there, if they don't have an associated package (shown in LANrev Server Center as the "Executable").
Try to avoid directly interacting with your packages root path file location at all --attempting to do so runs the risk of corrupting your LANrev installation,
That all makes perfect sense in a perfect world. In my world I have a directory that shows payloads of about 105 GB of data. In the console under LanRev Server Center I show a combined total for 22 payloads of under 2GB. Meaning that I have about 103 GB if data under the "LANRev Standard SD Files" Directory. I need to determine what files under this directory are orphaned from what the LanRev console is showing.
I need to remove any files that are not used by the product to free up unused disk space. This is why I need to have a tool, query, something that maps these files to actually being used and not just exist as orphaned content.
I would say you might want to consider a session with Ivanti Professional Services to resolve, then.
I was hoping someone from Ivanti was actually monitoring their forums to provide some guidance.
I hope they can help you with it...
My only other thought on that is to check whether you have added the available column "Payload Unique ID" to the Server Center Payloads window. That would help you at least ID the payloads you know you need to keep.
The file "PackagePayloadMappingList.plist" controls the mapping of Packages to Payloads, but once again, it was only ever intended to be managed by the Server process itself, and not edited or managed manually.
I'm not aware of any automation for resolving this available publicly, but Ivanti might have something developed in-house to help you. You'd have to open a ticket with them to ask.