I have been using Mendeley Desktop for about two years now. Passing trough a lot of modifications, Mendeley Desktop has recently come out of its beta state. The best research project manager software now seems more stable and faster than ever. Combing the potential of extracting the metadata of your PDF with the ability organize and synchronize them with the cloud, no better application seem to exist that can satisfy all these needs. Being a big fan of the application, though, there are a few critical features that I am looking for implementation in its feature releases. One of these is lack of Moving files while organizing files. If you use its file organization, it can only copy and rename all the files in the library to a single folder. This means that, you should have a duplicate of files every time you use this feature. To alleviate this problem, I use an application called Duplicate File Detective. Of course, there are many duplicate removal applications out there. But, I prefer this application for one main reason; it can detect and delete only old versions of your files.
Here is how how to do it.
1. Open your Mendeley Desktop and make sure your library as good as possible; Check the accuracy of the metadata; check for duplicates in side Mendeley; check the dates, author, title of your files.
2. After you make your library clean, go to Tools –>Option –>File Organizer. Check Organize my files. Click on Browse select a folder where you will store your whole library. You better select an empty ; otherwise, Mendeley will mix up your new files with the old files. You can also check Sort files into subfolders. But, I don’t recommend it.
Check rename document files as the above picture, and finally Ok. This will copy all the files in your library to a folder (named AllLing in the picture). As you can see it I am also putting it in the dropbox folder. The reason is clear. Dropbox gives more free cloud space (2GB) than Mendeley (500MB). You can also get more free space by inviting your friends to it.
3. Since the above process copies all the files from their original folder to a new folder, you will have two copies for each of your documents. To tackle this problem, now you need to run Duplicate File Detective. In the DFD, select the disk where you store all your files and click Run Project. When DFD finishes searching for duplicates, you will see all the duplicates in a window. Go to Smart Mark (circled red in the picture below) –>mark Old files in Each Group –>Mark By File Created Date.
Now, give a glance on the list of files. If every thing is alright, all the old copies must be selected while the new copies stored in AllLing (in my case) remain unmarked. You can then either Move or Delete them. Now, you have cleared your clutter.
4. You can fix a Watch Folder for Mendeley where you throw all new files that you will download from the internet. Mendeley will automatically import, extract the metadata , renamed and copy into Organizer folder (AllLing in my case.). After you make sure that the Mendeley has done its job, you can then manually delete the files in the Watch folder.