|go ahead... be a heretic|
Asking about things you don't understand is smart and good. Not asking is the dumbest thing you can do because it wastes everyone's time and you learn nothing and keep repeating the same mistakes.
I've always been taught that nice clean code, always has all variables declared before hand
I'd get a new teacher if I were you! Code with all the declarations lumped together may look pretty to some eyes, but you gain no advantage whatsoever from declaring variables like that. Always declare variables in the smallest sensible scope and initialise them at the same time. That helps avoid a whole slew of bugs including reusing a variable name and ending up with subtle heisenbugs as a result.
First, to answer a couple of questions you didn't ask. Use the three parameter form of open (open handle, mode, target) because providing an explicit mode ('>' or '<' for example) is both clearer and safer. Use lexical file handles because they are clearer and safer - safer because their scope is limited to the current block and using strict you are more likely to catch typos.
The point about avoiding nesting is that the deeper the nesting goes the harder it is to figure out what the code does. If you have a simple test and can bail (as in the next if line) you don't have to worry about that case any more, it's all done and dusted.
Slurping is where you read everything into an array. If that is followed by looping over the array using a for loop then very likely you can remove the array and use a while loop instead. That has two advantages: 1/ you can see from the code that you loop while there is stuff in the file (which gets sorta obscured by the array), and 2/ you only read one line of the file into memory at a time. Most often the second point isn't all that important, but if the file is huge it can be a killer. Neither reason is absolutely compelling, but slurping seldom has an advantage over iteration using a while loop so you might as well go with clearer and use the wile loop (iteration) form.
True laziness is hard work