LinkedList Fixes and Configuration Parser Improvements

LinkedList related commits are fairly self-descriptive.

While exploring the system for parsing configuration files, I noticed that the `parse()` method in Configuration.java was effectively useless at finding a config file when none was specfied. In attempting to search the given source file directory, it created an invalid path that actually included the name of the first given source file. In addition, the associated section looked like it might benefit from some more rigorous platform/architecture cases and general cleanup. The new code has been tested and correctly finds unspecified config files where the previous code did not.

It is worth noting that I do not yet fully understand the mechanics of `Main.class.getResource( fileName )`. To be safe, I have preserved this (for the moment) in case it does truly cover a useful case.