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What exactly do you want to do?
You cannot "run from sources", you always run compiled classes.
And you don't necessarily have to package the class files inside a JAR as you can see at http://confluence.jetbrains.net/display/IDEADEV/IntelliJ+IDEA+Plugin+Structure point 2 of "Plugin Content".
You could e. g. check whether the config directory is the normal directory or the sandbox directory, but this is not really reliable.
You could also introduce some constant that you set accordingly.
There are many ways to do many things, it would really help to know what you try to achieve.

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when I start IDEA with my plugin,  I need to identify whether it was started in "Development mode" ( I mean from Java sources/classes by the plugin developer) or in "customer mode" (that is when they install a JARed plugin)

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Let me repeat it in an easy way: Why?
If you cant or wont say why, I've already told you ways and why they are unreliable.

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I create my own SDK definition on plugin startup and I need to add "classes" folder when it's started in DEV mode. "customer mode" only needs JARs.

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I'm not sure I understand what you are trying to do, but you got my line with the link in my first reply? A deployed plugin must not necessarily have the classes in a JAR file, they can reside loosely in the ZIP distributable just fine as described in that link where I wrote in my first reply.

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E.g. specify a property in a run configuration?

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dammit!! :^O

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