Improve robustness across Atlantis models

[sgaichas]

The run_truth function assumes a standardized "output" prefix in addition to the Atlantis "scenario" name. Now users specify Atlantis output file naming conventions and do not always use "output" as a prefix. Need to update all functions to remove assumption of prefix and have users supply the output naming convention.

Assumptions about the functional group .csv input file are also hard coded into some functions such as load_catch and load_bioind that filter on functional group characteristics. "IsFished" was a standard column that has a different case "isFished" in at least one model. Need to update these functions to find this column even with different cases in the name.

[sgaichas]

run_truth in the annage branch no longer pastes "output"; the user must specify the full prefix.