The post below deals with duplication in the iTunes library. If I've understood your post you have duplicates in the media folder. Adding everything to iTunes and then deduplicating as described is probably the easiest approach at this stage.
iTunes may create duplicates if the same content is repeatedly added from outside the media folder when it is set to make copies of anything that is added to the library, or is added from an external drive that hosts the media folder that was offline when iTunes was launched.
Apple's official advice on duplicates is here: Find and remove duplicate items in your iTunes library. It is a manual process and the article fails to explain some of the potential pitfalls such as lost ratings and playlist membership, or that sometimes the same file can be represented by multiple entries in the library and that deleting one and recycling the file will break any others.
Start in the Songs view. Use View > Show Duplicate Items (pre iTunes 12.4) or File > Library > Show Duplicate Items (post 12.4) and then click Same Album to display exact duplicates as this is normally a more useful selection. You need to manually select all but one of each group to remove. Sorting the list by Date Added may make it easier to select the appropriate tracks, however this works best when performed immediately after the dupes have been created. If you have multiple entries in iTunes connected to the same file on the hard drive then don't send to the recycle bin.
Use my DeDuper script (Windows only) if you're not sure, don't want to do it by hand, or want to preserve ratings, play counts and playlist membership. See this thread for background on the script, this post for detailed instructions, and please take note of the warning to backup your library before deduping.
(If you don't see the menu bar press ALT to show it temporarily or CTRL+B to keep it displayed.)
The most recent version of the script can tidy dead links as long as there is at least one live duplicate to merge stats and playlist membership to, and should cope sensibly when the same file has been added via multiple paths.
tt2
