Yessss .... this has evolved hasn't it
Is this where you're going?
Search & remove tools for three groups of junk (to some) files:
calibre_bookmarks.txt (which some people will want to keep)
itunes plist/artwork (which I suppose somebody will want to keep
)
thumbs.db/.DS_store (OS artifacts nobody should want)
I think I missed some conversation, but are you going to search for these whether or not they're in the manifest and de-manifest them where needed if found?
Then, handled a little differently, search for & log & possibly remove unmanifested files (other than the cases above)?
That sounds really good to me.
I'd treat the itunes artwork just like the plist files.