How to Properly Remove iPhoto Alias Folders

Hello Team,
Over the many years as an iPhoto user, I have made many upgrades to my iPhoto Library. I have noticed that each upgrade comes with its quirks. The one that is recently bugging me are the alias folders that are created within iPhoto when you 'Show Package Content' in Finder.
For example, showing the contents of iPhoto shows that my files are no longer located in the 'Originals' folder, but now in a 'Masters' folder. I have a 'Library6.iPhoto' along with a 'Library.iPhoto'.
There are a few other alias folders that I'm sure came with upgrades since when I create a fresh iPhoto Library, none of those folders are present.
So my question is...  "How do I (or iPhoto) remove these folders properly?"
I'd like to have all the photo nice and clean with the most up-to-date file hierarchy and not some fragmented linking from yesterday. Why does Apple do this? Is there a good reason?
Also to note, I have tried copying a smaller library with the same issue and tried rebuilding the database, library, thumbnails, etc without any luck of making them disappear.
Thoughts??
Thanks!!

Was hoping there was an Apple sanctioned consolidation tool that would convert everything to the new heirarchy.
The "Apple Sanctioned" consolidation tools are the iPhoto Library First Aid tools. They will rebuild the iPhoto Library in exactly the way how it is supposed to be organized.
Back up your library, hold down the ⌥⌘ command keys, launch iPhoto and run "Rebuild Library". The result should be very similar to what you are seeing now. However, rebuilding shpuld only be done, if iPhoto is not working properly or before a software upgrade, that will reorganize the library.
If you want to access your photos, there are more versatile and safer ways than digging around in the package:
See Terence Devlin's user tip:                   How to Access Files in iPhoto

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