Check for conflicts in config files

[rs028]

This is related to issues #348, #355, #487 but expanded to check consistency of all input information:

1. variables can be either constrained, constant or initialized. If there are contrasting inputs the model should stop and alert the user or fall back to a default behaviour (some of this may already be implemented but is not explicit in the manual).
2. some variables should not be constrained, constant or initialized: eg. O2, N2, RO2.
3. some variables should not be in some output config files: eg. H2O, RO2 are always in environmentVariables.output, no need to have it in outputSpecies.config.