Multiple symbols can point to the same function, this means that when we loop over
the symbol list, we must deduplicate those functions being added twice.
Additionaly, we must also ensure that when we append a new type and set the type
index on a function, we must not do this again for the same function.

This commit also implements sorting of code atoms to ensure their order matches
the order of the function section to ensure the function signature matches
that of the function body.