Sure. I only mention OwnCloud as:
1) It's open source so you can see how they're approaching things and learn from it, even if ultimately you don''t use a single line of their code
2) You can use it as a starting point to build your own app (assuming you're okay releasing your code under the GPL 2.0 license)
Trying to get Dreamweaver to play file manager and syncing utility with an online custom-built web app...is...well, I believe it will ultimately be a frustrating experience as Dreamweaver isn't designed or built for that. It's really an IDE for web designers and web developers that just happens to have FTP functionality. Frankly there's better apps when it comes to FTP/syncing functionality. I'd say you'd have a better chance of success with creating shell scripts (powershell or bash) to ssh into your server, run some form of diff/versioning, and sync files.
>However, as I save the file in a different folder, clicking
>FTP upload will not simply put that file on my server
Is the folder within the defined site (a subfolder in the site) or external to the defined site? DW only manages files within your defined site. If it's external, then you would either need to create a new site definition, or use another FTP client.
I agree with bemdesign; DW is really a poor choice to use to FTP files unrelated to your site. There are much better and more flexible FTP clients out there. Once you do have your files on your site, you can certainly use PHP or any other server side scripting to list your library of files.