Configuration in run.conf is used from other scripts than run.sh. For example shutdown.sh or twiddle.sh include it. They should not because that leads to undesireable or even dangeous effects.

Details:
Editing run.conf an including
JAVA_OPTS="$JAVA_OPTS -Xdebug -Xrunjdwp:transport=dt_socket,address=8787,server=y,suspend=y"
to enable remote debugging

Starting the server:
sh run.sh -c minimal

Stopping the server produces:
sh shutdown.sh -S
ERROR: transport error 202: bind failed: Address already in use ["transport.c",L41]
ERROR: JDWP Transport dt_socket failed to initialize, TRANSPORT_INIT(510) ["debugInit.c",L497]
JDWP exit error JVMTI_ERROR_INTERNAL(113): No transports initializedFATAL ERROR in native method: JDWP No transports initialized, jvmtiError=JVMTI_ERROR_INTERNAL(113)

This may get worse if someone uses a -Xms3000m setting on a server that only has 4GB of memory. Potentially leading to a swap out of a production system to disk.