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Suggestion for Flashbuilder GitHub configuration for forked viewer and forked widgets

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I am trying to decide how I want to setup my Flash Builder projects to deal with customizations to the viewer code and customizations to various widgets.

I'm familiar with Flash Builder enough that I've used it to customize versions of the viewer and build widgets in the past, but I'm new to GitHub. I've forked the 3.3 viewer and am going to make some changes to it. I want to download some widgets and make some changes to them as well as make some new widgets. It seems to me that the custom widgets and the viewer should be in their own flashbuilder projects so they can be debugged independently and changes can be managed in github independently as well since they are independent objects. I've only done this as one big project previously with my custom widgets and custom viewer as one project. I haven't found a good description yet of what a best practice would be for this.

Should I simplify it and leave it as one thing or break it up? If I break it up what do I need to do in flashbuilder to be able to debug only the source code of the widget, include a stock flexviewer with it?

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