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answers:

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I have developed various Java EE web-applications in Netbeans by selecting webapplication as the project type.

Now, I want to start coding a web-application in Eclipse. The application will be based on Struts framework.

The structure of the project created by Netbeans and Eclipse are different.

Q1. What project type I should choose for the above application in Eclipse? I chose DynamicWebApplication as the project type.

Q2. Which project structure to use for the web-application?

+1  A: 

The project structures are arbitrary - as chosen by the IDE developers.

DynamicWebApplication is a fine choice for web-app.

Leave it to the IDE to form your structure and subsequently automate the build process.

However, I'd suggest another option for structure & build process - Maven2 - it imposes a different structure, but provides easy dependency and build management.

Bozho