I thought you were building a package, wrote the following, then read your post again. This may be of no use to you at all. Where there is face, there is palm.
I had the same problem recently, I'll list the steps I took to sort the problem. The explanations might be a bit crappy so I'll make a video when I get chance.
1. Searching the meta.json file for the dependencies:
Prep & run the package in the package builder & make a note of any licenses you don't recognise.
Open the folder you have just created - it is in the add on package builder folder located in the Vam Updater folder.
Open the meta.json file in notepad.
Use the find function (Ctrl+F) to search for the names of the dependencies.
If the dependency is inset in notepad it is linked to whatever is above it. I'm on a phone & can't remember the exact format but it's something like this:
,
[Main.dependency.1]
(information)
, ___ ,[Other.dependency.1]
, ___ ,(information)
, ______ ,[Other.dependency.2]
, ______ ,(information)
That should help determine whether the dependencies are referenced by something from another add-on package.
2. Searching morphs
Sometimes creators may include morphs in their add on package which will also reference other things in that particular scene. If you have previously downloaded a Wolverine333 scene you could have your work cut out.
Open the morphs menu in VAM. Search all directories and check the 'active' filter.
Look through the list of active morphs and check the origin of any shown in red (when a morph is coloured red rather than grey it has come from a package that you have downloaded).
Hover the cursor over the package icon on the red morphs to see the package it is from. If it is from a morph package then all is well, if it is from a scene then you will probably be able to use another morph in its place which will stop the offending dependencies being referenced.
3. Searching clothing & hair
This is pretty much the same as with the morphs but done in the clothing menu / hair menu. Set the filter to show only active items & select the package icon to see whether anything else is being referenced with it.
Open the package builder again, add your files etc & repeat step 1 if there is anything remaining.
I'm not sure anyone will make a plugin for this.
Due to the tedious task of solving the issue, most creators are only going to do this once then never again. I spent around a month making 5 pretty complex scenes which loaded one after the other before running the package builder & realising what I had done, so can say for certain it is a mistake I will not make again. If this doesn't solve it & I forget to make the video, please remind me to do so.