To generate the documentation from the command line use the example presented below.
java -cp "ECLIPSE_PATH\plugins\org.eclipse.equinox.launcher_XXXX.jar" org.eclipse.core.launcher.Main -application org.eclipse.gendoc.batch.GendocBatchMode -data d:\workspace_directory -idt dir="D:\your_template.docx"
Where:
All the directory paths are absolute.