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I'm releasing Gdn_Scaffold shortly on an MIT licence, which is a utility/script which will help your organise, often cluttered plugins.
Requires php >= 5.2 to run
For those that already have IDE templating and automation regimes, you probably don't need this. You might want to look at the utility methods though.
What it is NOT for:
You can use on a plugin that needs some organisation, or a new project.
It is a scaffold it does not make your plugin automatically work, you need to implement along the lines suggested.
Treat it like beta software. It does backup within the plugin file, but it is not substitute for an external backup regime.
This is a tool/helper, don't trust it to be perfect.
grep is your friend.