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I would like to treat the great reports generated by metric_fu as documentation and keep them in my repository. So how do we convince it to save its output in doc/ instead of tmp/ ?

Stew Welbourne has the answer:

MetricFu::Configuration.run do |config|
  config.base_directory     = 'doc/metrics'
  config.scratch_directory  = File.join(config.base_directory, 'scratch')
  config.output_directory   = File.join(config.base_directory, 'output')
  config.data_directory     = File.join(config.base_directory, '_data')

  config.saikuro  = {  utput_directory => File.join(config.scratch_directory, 'saikuro'),

  # the rest of your configuration goes here
end

Just make sure that your new target directory is two folders deep, as the original tmp/metric_fu is, or you may get in trouble with the graphing part of metric_fu. Voilà!