Allow specification of counterflow composition and temperature

This allows, for example, simulation of premixed flames supported by
an inert high-temperature counterflow stream.
Move reading of initial profiles into Python
Set counterflow mixture composition to equilibrium

When this is not done and the counterflow temperature is high, the
boundary condition is not consistent, and the domain is repeatedly
expanded in an attempt to compensate.
Rename source files for "strainFunction" to "scalarFunction"
Make error message after failing configuration test more useful
Rename "StrainFunction" to "ScalarFunction"

Rename descendant classes as well. Want a more general name before using these
classes for other purposes.
Fix some integer size / signedness warnings
Add option to scale reaction rates as a function of time