making $PACKAGES_DIR a local variable and adding warnings about shared variable names at the pipeline level

making the DOckerfile a template, people using it should make a copy and override the UID and GID variables for their machine

making the DOckerfile a template, people using it should make a copy and override the UID and GID variables for their machine

making the DOckerfile a template, people using it should make a copy and override the UID and GID variables for their machine

So that coordinator tests work with ews-epidemiology commit d344567 .