Also, removing the file system tree would be a huge step backwards. Organizing hundreds or thousands of files between dozens to hundreds of projects is just not suited for a "everything in one searchable bag" for a few reasons: To find something with search, you have to already know what you're looking for - something that browsing a folder solves instantly (how can you know you see all relevant files with a search? Maybe there's an important file that didn't match your query?!) - and the common "solution" with tagging/labels are just single-level folders in disguise....
I'm glad Apple decided to not port OSX to the iPad, or replace OSX with an iPad-esque iOS. Most people I've talked to that experienced windows 8 would agree that when Microsoft did just that, it was a misstep.