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change directory of where files are written
I installed fortify as root and thus when users use the product vi tomcat it wants to write files to ~root/.fortify. Is there way to change this location?

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When using Tomcat, you can specify the Fortify SSC home directory for the user through the {-Dfortify.home} option added to the JAVA_OPTS variable in Catalina.sh.
As an example within catalina.sh:
JAVA_OPTS="$JAVA_OPTS -Dfortify.home=/home/user_name/some_directory/fortify_ssc"
Here is an addendum I received internally for your question.
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As far as I know the Fortify home directory is created based on the user that is actually running the software. This may indicate that they are running either SSC (Tomcat) or SCA as root, which in general is considered a bad practice. So instead of using some properties to modify the Fortify home directory location, they should actually be fixing their setup to not run the software as a root user.
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Micro Focus Fortify Customers-Only Forums – https://community.softwaregrp.com/t5/Fortify/ct-p/fortify