Actually it's not too hard to work out - web based IDEs are not new, if it helps you could think of C3 as functionally a CMS for game development.
As C3 is linked to our accounts, I imagine every account will have a cloud based file tree storing every from c3 files to image assets - most importantly, there'd also be a folder for plugins.
Where it gets really interesting is that because everything is the browser and behind an account login now, adding extensions should be completely seamless - you'll be able to pop into the Scirra store mid development, install the plugin you need and get right back to development.
Christ where it gets really exciting is when you consider all the new ways going in browser opens up C3 for the community, you could possibly:
1) Have a baked-in "Post to forum" option within the program. Having a problem with a tricky event? Forum support is a click away.
2) Share file access across accounts for collaborative or educational gain.
3) Tie in seamlessly with version control platforms like GitHub for professional level collaboration options.