Better warnings & warning/logging infrastructure

[brown170]

The code should issue more warnings, especially instead of raising parsing exceptions. At the very least for some specific situations:

• Institute parsing
• Reaction parsing
• b/sr for SIG (why?)
• Not implemented observable handlers

These need to be exposed (appropriately) during unit testing, suppressed by default under normal operations and controlled tightly and monitored when checking files

[julia-sprenger]

This sounds like a good use case for the logging module.