My Library is already partially organized (manually) with regular filesystem folders. But it is pretty messy right now and getting unwieldy. Also several files should be renamed to something meaningful (right now paper titles-author-year is best for me). I am wary of pulling the trigger, Mendeley may make things worse, not better.
Any opinions? Experiences? Thanks.
I've personally used this feature, and I really like it - though honestly, part of the value I get from Mendeley is that I stop worrying about my files and folders and just use the software itself most of the time. As I have it sync them up I'm not even really concerned with where it stores them any more.
My recommendation is just to copy-paste your directory of files to a separate area "just in case", then fire away. File naming is (was) a pet peeve of mine, and I really like to have the files nicely named so I can search them - then I usually also sync that folder to Google Drive so I can access my documents anywhere (phone, guest account, etc).
It's a useful and nice feature, but honestly I found less value from it than I expected precisely as I began using Mendeley more. I still use the feature, but the other things the program does make it almost redundant - but still nice and I'm glad its there.
Mendeley has always like to describe themselves as "Opens up Science for Everyone", but their EULA is very restrictive (e.g,. see my question on Open Data.SE). Mendeley is now owned by Elsevier. Many people felt betrayed by the move (cf. this article in the New Yorker).
Academic careers are long and I would be very hesitant about putting my library of articles in a closed source system with a restrictive EULA that is owned by one of the major for profit publishers. While Menedely might be better than your current system, it is unlikely to remain the best system over the next 30+ years. You might be better served by developing your flexible system for keeping track of articles.
I am not aware of a FOSS clone of Mendeley (see Free, open-source substitutes for Mendeley?), but FOSS projects like JabRef and Zotero might meet many of your needs and provide better flexibility going forward.
Mendeley does this quite well. The options for folder organization are any combination of author/title/journal/year, in any order you want. The options for file names may also include any of author/title/journal/year, in any order, where you can separate by underscore, hyphen, comma or period.
One thing which could be improved is that Mendeley will not let you change the format of individual fields. For example, for author names, if there are up to 3 authors it will have all author names (e.g. "Johnson, Cohen, Livingstone_Nature_2013.pdf") but if there are more it will write it as "Johnson et al._Nature_2013.pdf". Also as you see it uses spaces and commas. So if the exact formatting is very important to you this may be a problem.
Note though that Mendeley has a special site where you can ask for new features and follow up on their progress. It works pretty well, though the timelines can vary (took them ages to get an android app).
As BrianDHall mentions, there are many other better reasons to use Mendeley - I definitely recommend it.
