Clean up and document compile time options

[kafitzgerald]

Potentially worth addressing along with issue #230.

Given that for most compile time options we have some fairly clear recommended defaults, it would be nice to come up with some well documented and justified default options and implement these (if not already done). This would eliminate some user / developer confusion and potentially the need for the template with compile time options listed.

With the exception of large file support this may just require documentation updates and minor changes to the offline compile scripts.