Organize related files into subdirectories, and remove pointless settings file.

This pull request includes a simple reorganization of multiple related files into well-named subdirectories within the package. 

The settings file has been removed, because it has no effect on the ST2 bundle by simply naming a file extension. Note that syntax highlighting is activated according to the filename extensions specified in the syntax file. ST2 setting are for specifying certain behavior, such as tab stops, and so on (see the ST2 documentation).

The underlying motivation here is to pave the way for a new Commands subdirectory, which I intend to include a new command that creates a new PDE-based Processing sketch (with named directory and main .pde file) and another command for creating "pure Java" Processing programs with a boilerplate project template.

Having directories for each part of the package just keeps things tidy.