This feature has been brought up before, as having directories does make a lot of sense. I originally opt'd for the flat filesystem due to the simplicity to implement and manage.
I mentioned to another beta tester that I was debating hotly on the API for file system access. During the beta, there might be a testing phase where a block-level API will be available. This will enable the creation of completely custom file systems, with and without directories, or no file system at all.
Essentially the running KERNEL reads and writes RAW bytes to/from the disk and memory. Programs would use an API the kernel provides to read/write files, so the RAW bytes portion is entirely abstracted.
This will also make the game more realistic, as you can literally create Norton Utilities type programs where you can explore the RAW sectors of the disk, and see deleted files, or hide code on disk without a file attached to it.
Look forward to this during the closed beta, as this cannot be tested/implemented afterwards.