We are using hpexstream product for customer communication. we like to know what are the pub files and why are they used and also want to know if we can have the custom dotnet(c#) jobs and also we want to know how to do deployment of these files and jobs to the higher environment
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Pub files are compiled packages holding one HP Exstream "application" each. They are created in Design Manager and Designer, which get their elements from a database. After a pub file is created, it can be deployed to a server, production environment, which holds HPE Engine with all the necessary configs, automation scripts etc. Engine is the central part, which gets run with a data file, pub file, configs etc. to do the actual work - create visual documents, ready to be distributed to clients by whatever means.
As far as I know, external code (C#) is only usable together with engine if you exchange information via files.
Deployment needs some automation set up, so the Engine gets started whenever you need and in the way you need. How you set it up is up to you. Probably OpenText customer service can help you, they hold the legals on the software now.