The files you need to change are for an upgrade to NetLogo are:
If N.x.y is the release of NetLogo
- edit
jar_manifest.txt
- to update the NetLogo extension to N.x - copy
netlogo-N.x.y.jar
tolib
from the Netlogo tree - in
bin/build.sh
update the library path to pick up the file just copied intolib
- change
bin/run.sh
to pick up the new version of NetLogo