Build the migration tool
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* right click on the org.eclipse.acceleo.aql.migration project
* Export > Java > Runnable Jar file
* Launch config: Migration Launcher
* choose an export destination & a jar name, e.g. "migrator.jar"
* check the "Copy required libraries..." option

Launch the migration tool
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 java -jar <myproject>/<sourcefolder> <output_folder>
e.g. from the folder containing the Acceleo project myProject:
 java -jar migrator.jar myProject/src output