Gh245 fix

Some changes to address gh-245 and clean up related code. I think it's a good solution though not particularly elegant. Passed my own tests, i.e. meta-analysis was updated when forced or required based on check criteria, but would not waste time converting traits only to find that they hadn't changed and no update is needed. 

Also passed `build.sh --install --test`. The `--check` option fails for me but that seems to be a separate issue.
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