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Huge size for a stand-alone java swing app

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I have 13M jar file containing all the class files of the application as well as the dependency libraries.

With Smart Optimization preset, java run-time slim down and a medium runtime  reduction, a self-contained directory backend comes around 90M.

Is there anything else that can be done to reduce the disk foot print?

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Why do you care about the disk footprint? Would you like to distribute your application on flash memory?

Honestly speaking, 90M sounds unfeasibly taking into account the techniques that you employ: it should not be more then 50MB.

How big are the executable and "rt" folder separately?

For disk footprint reduction, you can reduce inline expansion method (to minimum or tiny methods only), and enable high disk footprint runtime reduction in addition.

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