first pass through supporting failure recovery

core_diversity_analyses.py now checks for the existence of output files before creating them. this allows us to re-start failed runs without re-running everything.
added support for failure recovery at the script level
added logging of skipped analyses

this is useful for understanding what happened and didn't happen in a given run
added note on new features

partially addresses #688
modified based on input from @jrrideout
Merge pull request #973 from gregcaporaso/core-failure-recovery

Core failure recovery