The PHP file system functions are largely based around the Unix/C system, so you can pick up any Unix reference manual to learn more about how things work and why. If you really want to dive in and get very specific information, consider William Von Hagen's book, "Linux file systems" - it is very (very!) technical, but a rewarding read if you really want to know how things tick.
Similarly you can try "Unix Shell Programming" by Stephen Kochan et al - it is a slim and easy to read book that should give you an idea quite how close to general Unix and C programming PHP is. Of course, this works in your favour if you ever want to try out C programming!