Choose PasDoc output directory
Use CommandLine option --output DIRECTORY (short form is -E DIRECTORY) to tell PasDoc where to write the output file(s). By default PasDoc writes output files to the current directory.
Note that the output directory in not created automatically. Make sure that it exists first. For example, on Unix, use mkdir -p … like this:
mkdir -p doc/ pasdoc --output doc/ MyUnit.pas