You can debug remote server for example from eclipse using JPDA.
For this you need:

in eclipse:
1) just open debug>debug configurations> remote java application

in tomcat in windows we have bin/catalina.bat or in linux bin/catalina.sh

2)  in file head

catalina.bat
set JPDA_ADDRESS=8000set JPDA_TRANSPORT=dt_socket catalina.sh export JPDA_ADDRESS=8000export JPDA_TRANSPORT=dt_socket
3) change last line catalina.batcall "%EXECUTABLE%" jpda start %CMD_LINE_ARGS% catalina.shexec "$PRGDIR"/"$EXECUTABLE" jpda start "$@"