Better error handling in inner functions

[jakewilliami]

We should handle errors better in internal functions. E.g., see SystemError and Base.IOError. See also how realpath handles non-existent paths.

The worst case scenario is that we seg fault, as we are passing around pointers within C calls. Let's try to avoid this (at the very least) at all costs.

[jakewilliami]

Part of this is better checking of output in all of the ccalls we make. E.g., here.

[jakewilliami]

Another aspect to this is ensuring that we check the expected return code (e.g. 5ce791e).