I suggest you ...

Use the real location of the files (HD folder structure) to construct Mendeleu folder structure (colections)

Imagine use the the data of the tree of folder that the user already have (the URL of the files) to build the Mendeley collections folder tree.

Most of the user, before begin to use mendeley, build, over years of research, a extensive tree of folders to organize all the documents.
Mendeley could use these data to build a tree of folders (mendeley collections).
With out this feature is impossible to reorganize thousand of documents that are in a pool (after drag and drop the library folders).
The editions made on the mendeley folders could be implemented on the real folders.
It would help new user to join and love mendeley

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