@dambaras @duderonomy I second Zotero - you will need a way to save and later access metadata of your documents & filenames are a poor solution for that.
(I'm not saying it can't suit your purpose)
And using Zotero it's very easy to keep the same file in different collections...
There even is the possibility for automatically renaming of the file based on metadata :)
Yes, but you don't actually need the storage for you files - just for the database (of metadata).
You can link to files on your local machine; and even use relative linking.
I'm using a different cloud for synching my files (and point zotero to the right directory on each machine) und zotero-sync for the database.
300MB ist enough for a database containing thousands of entries