Brown University has developed an IDE for Java called Code Bubbles that takes a pretty radical departure from current IDEs. While most IDEs, such as Eclipse are file-based, Code Bubbles is based on fragments. The system appears to support reading and editing code with fragments, multi-tasking, annotating and sharing, and debugging with bubbles. There's a website with video too.
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You are likely thinking of Robert Zemeckis
http://www.imdb.com/name/nm0000709/
known from movies like Back to the Future and the Frighteners but not really for any of his other movies.
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Most decent IDEs do that (regardless of language).
This just takes the idea one step further and manages the files as well.
Personally I want to dislike this as thus far I've been very disappointed everytime I hear the phrase "new IDE design", however I'm actually quite impressed from the video. I'll be keeping an eye on this project for sure.
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It's almost certainly just .java files, but the fact is you're not creating the files and managing the contents yourself so the software must be doing it for you.
At least that was the logic I applied - I guess it's a matter of interpretation.
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Would be nice to link this up with GUI layout tools.
I sort of like using graphical layout tools for user interfaces. Then I end up having to edit the generated code, or in the case of Glade match up the components and signals with their callback functions. I hate that part, all the switching back and forth.
Something like this would be so much nicer.
Also the video focused on an existing codebase, and not on writing new objects from scratch. This is probably where the clear and immediate benefits are.
If I used this, I would need to ask procurement for two 30" monitors too.
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Indeed innovative, and possibly has the potential to be interestingly productive. Obviously a lot of work went into this project, and it looks really good. Well done 
Wishful thoughts:
1. Allow resize of scrollable bubbles (object properties, docs, etc).
2. Allow other languages via plugins (syntax, code analysis, compiler/debugger, docs etc), and hopefully also dynamically typed languages (such as Javascript/PHP/etc - probably with reduced functionality which depends on static typing).
One potential issue that might arise when people actually start to use it, is managing the huge amount of contexts/layouts/states that can be stored using this system.
While the system does provide a solution, and in a way, is the solution for context-based programming sessions, it still seems to me that it has the potential to drown the programmer with so many contexts that it actually reduces productivity. But then again, it has to be tried for a while before such statements can be expressed.
Overall, extremely interesting. Looking forward to try it out with languages I use more.
Again, Well done
