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Packages within a web application, best practices, organizing large projects  RSS feed

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Linux Tomcat Server Ubuntu
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I am using a full web application from Murach's JSP 6 to learn Servlets. Additionally I am building my own projects now. The project/s I am building have CRUD interfaces for around 30 tables on SQLserver. The project will be printing 15 kinds of reports using the data from the tables. Eventually the reports will have a PDF option, too. This application will be on a LAN not on an external web site. The server is Tomcat 6 on Ubuntu and I am coding in Netbeans 7.2 on Windows. I have some questions about organizing servlet projects with many files and about using packages.

1) Is it better to break a large application into small projects or keep it as one project since many classes for the SQL data will be used by the multiple reporting classes and other CRUD interfaces. For instance some of the small tables are reference lists that become list boxes for a line item.

2) How should the packages be organized within the project?

What I see in the Murach project is that the packages are organized by function.

In frameworks I have used in other languages the classes are grouped by the data they are handling and then some other classes might be made for reporting.

Same question for the JSP's under WEB-INF, they seem to be organized into sub-directories by function.

Are there best practices for project organization or is the organization left to the company's development standards?

Would the packages and subdirectories be the same in Eclipse?

Thank you,
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