Fix base_formatter specs
Fix cane specs
Fix flay specs
Fix flog specs
Fix reek specs
Fix roodi specs
Fix saikuro specs, but they are weird
Fix rcov specs
Allow replacing or modifying metric run_options
Update .metrics file to reflect new code
Fix graph directory bug
Rename graph engine config to GraphEngine to avoid name conflict
Fix grapher bug, grapher specs
Fix result specs
Fix some of the run specs