Do not cleanup logs, lib and temp folders from base template at install time

Without logs folder new instance start was failing with this error:

touch: myinstance/logs/catalina.out: No such file or directory
/usr/local/Cellar/tcserver/2.9.3/libexec/tomcat-7.0.42.A.RELEASE/bin/catalina.sh: line 387: myinstance/logs/catalina.out: No such file or directory
Status:                NOT RUNNING