Config Files in Home Dir

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I maintain a package that when run for the first time creates a file,
~/.projectM/config.inp.  The package previously needed symlinks to
fonts because the location of the fonts was hard-coded.  I have since
removed the symlinks, and patched the package so that config.inp will
be created pointing to the real font files.  However, when one
upgrades from the previous version to a new one, the config.inp file
still points to they symlinks.  What is the appropriate way to deal
with this?

Thanks,
=-Jameson
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