settingsUsed.txt lists default values of application.properties instead of actual ones

I see misleading situation where
settingsUsed.txt reports default values of keys listed in data/config/application.properties,
in place of those actual values.
Currently, we have to parse output/hgcaa.log to check what values of data/config/application.properties were actually used.

Start by locating the code that generates settingsUsed.txt and compare its values with the resolved settings from data/config/application.properties. Use output/hgcaa.log as the reference for the values actually used; done means settingsUsed.txt reports those actual values rather than defaults.

Written by the indexing model from the issue text.