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To use jADT to generate Java from the shell use you'll need to download the executable jar jADT-core-0.3.0.jar.
java -jar [path to /jADT-core-0.3.0.jar] [source path] [path of directory to receive the output], e.g.
The source path can be either a directory with files ending in .jadt or it can be an individual file.
java -jar lib/jADT-core-0.3.0.jar src/main/jadt/ target/generated-sources/jadt or java -jar lib/jADT-core-0.3.0.jar src/main/jadt/MyStuff.jadt target/generated-sources/jadt
If for some inexplicable reason that doesn't work for you, then
java -cp [path to /jADT-core-0.3.0.jar] com.pogofish.jadt.JADT [source path] [path of directory to receive the output], e.g.
java -cp lib/jADT-core-0.3.0.jar com.pogofish.jadt.JADT src/main/jadt/ target/generated-sources/jadt