Can we convert any java program to an eclipse plugin?
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I would suggest starting writing a plugin. Eclipse has its own view of the file system. You can save a lot of work and hassle by using this API directly. And the result will be much better integrated into eclipse.
You can start reading about the API here: http://help.eclipse.org/galileo/index.jsp?topic=/org.eclipse.platform.doc.isv/guide/resInt.htm
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To a great extent. It's just a matter of adapting to the set of APIs laid out for plugin development. If you are developing your program in a modular way, going from standalone to plugin shouldn't be too difficult.
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