I've read this question and it is not a duplicate to mine. I have a .exe file which has different contents inside when opened with 7zip. However let's say I know that it uses EXE4J, how can I decompile it and get the jar out of it?

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EXE4J creates a temporary folder to store the JAR. So using process monitor I was able to locate the JAR file.

Here's how I found the answer

So as I was searching I found this useful GitHub page (It should help you find the main class), and as I scrolled down in the Embedded JARs I found

This script does not extract embedded JARs, it only finds their offsets. Use 7zip on the file to unpack embedded .jar files. Alternatively, execute the file and grab the JAR from the TEMP folder. It is named e4j_xxxx.tmp

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