Surely you don't get the same level of organisation (particularly hierarchical) by having everything in one file? And doesn't that mean you are constantly scanning up and down the file?
"Search" is my friend to move around in my one big file.
I think of it like a the same shift introduced by Google Mail with their "label" thing. At the time it was quite disturbing, we used to classify mails in hierarchical directories. Nowadays, when I want to retrieve a msg, do I navigate a directory structure? No. I just "search".
