I want to distribute a swing app to my client. In that application two property file are there, which should be visible to client so that they can edit, I can not give it as runnable jar. Also I want something like apache-tomcat zip file which once you extract it will arrange folder structure also will give property file to edit and on next run it reads that property. Also apache-tomcat starts with startup.bat or startup.sh like that I also want.
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If I understand you correctly you want a tool to make distribution package for your application. That generates folder structure and unpacks application and data files to this structure.
There are many free and commercial setup builders. I think you would prefer multi-platform builder, so look for java setup builder.
Check this thread, this question was discussed there.