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If you are asking whether by creating a script to generate/publish a master project will automatically generate/publish the slave projects, then the answer is no. You'd have to create the script to generate/publish the master AND the slave projects to the required locations.
From our testing, the CLI uses the Generate and Publish location settings from the Default Layout, unless you use the location "flags" to indicate other locations.
Ultimately, we decided against using a script for doing this in a 40-project merged WebHelp situation because of fragile network issues.
No. I was asking if I specify a location to publish too, then call the RHCL.exe from the command line with the appropriate flags, if it will generate then publish. The script already generates the appropriate projects in the appropriate order, but having the script copy the files over is adding significant time overhead. I was looking for affirmation that the option to publish occurs automatically if a destination is specified. I think the answer is yes.
I'm also having problems with the output not synchronizing when viewed as a URL, but I think that is a seperate issue.