High-level design documentation.

As part of the developer documentation we need high-level design documents. Specifically I'm thinking:

• How does NWX fit in with the current software ecosystem?
• How are the major pieces structured?
• How does a major internal (all modules owned by NWX) workflow, such as a single point calculation work?
• How does a workflow involving external (code not owned by NWX) codes work? As an example, QM/MM with MM being provided by an external code.

The last two items should be pseudocode-like and are meant to flesh out the pieces of the workflows more than anything else.

Where relevant we should document explanations for decisions appearing in the aforementioned designs. Some examples:

• Why object-oriented programming?
• Why a top-down design?
• Why is the major language C++?
• Why use Python for the APIs?
• Why so many repos?
• Why a module system?
• Why separate the APIs from the framework?
• Why do we need Mokup?
• Why are the module collections partitioned as they are?

These are high-level design documents. They are not supposed to go into the nitty-gritty. Generally speaking the designs discussed here are project-wide and are somewhat orthogonal to how each piece of the stack actually accomplishes its goal. For example, design details pertaining to exactly how the classes in Chemist or PluginPlay work are out of scope of this issue. That said design documentation is needed for the entire stack (including classes in Chemist and PluginPlay), but will be done as part of other issues/PRs.