Apache Tomcat has an optional script for setting environment variables. In the documentation, it says "all environment variables can be specified in the "setenv" script" (.bat for Windows and .sh for Linux).
Section 3.4 in https://tomcat.apache.org/tomcat-9.0-doc/RUNNING.txt
Since it is a script and not a static configuration, the properties file can be created from it. This patterned works for me for an environment configured S3 connection, but here it is re-written for your example, along with the bonus of how to set the properties file's location:
cat > "${CATALINA_HOME}/conf/application.properties" <<EOF
pathToInputFile=${TOM_DATA}/data/incoming/ready/
pathToInputFileProcess=${TOM_DATA}/data/incoming/work/
EOF
CATALINA_OPTS="${CATALINA_OPTS} -DTOM_DATA=${TOM_DATA}"
CATALINA_OPTS="${CATALINA_OPTS} -Dapplication.properties.location=${CATALINA_HOME}/conf/application.properties"
export CATALINA_OPTS
You may already be using this file if you configure runtime things like memory constraints, headless mode, or which garbage collect to use.
NOTE: the documentation has caveats about when setenv would not be called and some exceptions as to a few environment variable that cannot configured in it.
application.properties
? – Burberry