Debian – Real time cmd tool to show HDD space remaining

A filesystem overlay would probably work better for this. Using something like aufs you can create a 'virtual' directory out of several combined directories. You can configure whether writes should propagate back to the original directories, or use a copy-on-write method to leave the originals alone, or disallow writes altogether.

However to answer your original question, you can use something like lsyncd to trigger an rsync as soon as a file is modified. lsyncd uses rsync, which is capable of syncing directory contents without keeping the directory name. Generally the way to do this is to sync sourcea/. to /some/destdir/. The important part is the dot at the end of the source path. This is a general trick that can be used for things other than rsync, like cp.

This sounds very much like the approach taken by RTLinux, which still seems to be available but not commercially supported.

That being said, there's a community unto itself about real-time Linux concepts, and the CONFIG_PREEMPT_RT patch would seem to enable the functionality you're looking for. As with all kernel hacking, do so at your own risk. There's a HOWTO available to help you get started.