Thanks for the question!
If you use the remote analysis options in the Polyspace user interface, the results are automatically downloaded after analysis and the report generation should occur fine.
At the command line, you have to explicitly download the results using the polyspace-jobs-manager command using the syntax:
polyspace-jobs-manager download -job ID -results-folder FolderPath
Once you submit a job, the compilation part of the analysis runs locally. Then, the data is submitted to the server. After submission, the results folder contains a file ID.txt that gives you the job ID (or even at the console, you can see the job ID). You can use the command polyspace-jobs-manager listjobs to check if the job with your ID is completed. Once completed, you can download the results using the above syntax. Then, you can use the polyspace-report-generator command to generate a report from the downloaded results.
As you can see, this is not as friendly as the automatic download and report generation in the UI. There are two stages where you have to implement some sort of spooling: check if the compilation is done and an ID is available, then later check if the job has completed on the server. If you are comfortable doing that, you can write a script that will do this. The desktop workflow was mainly designed to be interactive. So, even if there are commands available, it takes quite a bit of work to put them into a script where everything would be automated.