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By default yofi locally collects usage statistic, i.e how much certain application has been launched. Then the default view reorder the entries based on the usage.
The files are the following:
Apps mode: $HOME/.cache/yofi.cache
Bins mode: $HOME/.cache/yofi.bincache
The file format is simply a list of lines with usage number and its entry name (binary or desktop file). These files can be freely edited to change the default view order.