Convert SIPNET compile-time flags to run-time options

[Alomir]

Once Decide on fate of compiler switches is complete, update SIPNET:

• Flags slated for removal: remove flag and all related code
• Flags slated for "always on": remove flag and all "flag off" code branches
• Flags slated to stay as options: convert to run-time options

For the flags that are being converted,

• expand the existing command line option code to include them
• add checks for exclusions and dependencies between options
• expand sipnet.in handling to also handle the same set of options as config-file params; note that specifications at the command line override those specified via file
• (likely) add a context struct or the like to track all of the config that is specified; possibly add source of specification (file vs command) in there. We will eventually want to log that info.

See issue #72 for discussion of current compile flag exclusions and dependencies (but note that list may not be exhaustive).

PR #96 Covers the first part of the above, but is not enough to close this issue.

[dlebauer]

We've reached consensus in #71 (comment)