Local variable cleanup

First batch of formatting fixes, submitting these before things get massively out of sync again.

I've tried to apply the following rules throughout the code:

 * Local variables should be declared within the scope in which they are used.
 * Read-only variables should be declared `const`.
 * Local variables used in only a limit range of the scope should get their own scope.

I've also tried being a bit more explicit in variable and function naming.

See merge request !113

Conflicts:
	src/engine.c

size_t

As per #70, we will run into problems with more than 2bn particles per node as all the particle counters and loop variables are currently `int`.

As a first step, switch the stored particle counts to `size_t`.

The next series of commits will be to change all the *loops* over the particles. I'm breaking this into two pieces since these changes are highly disruptive, especially since I'm submitting them along with !113.

See merge request !114