We have a site that we want to try deploying on Apprenda, it mainly hosts .exe and other installation files for various applications (it’s a software depot). Can we upload these files as part of the archive upload? And if so, can we upload additional files in the future without having to re-upload all current files (delta upload)?
You can upload those files as part of the archive to an extent. What would be the archive size? For this type of use case, I would recommend hosting the files in a share somewhere and hosting on Apprenda a website that links to those files. The cloud is not mean to work as a repository of files since you will add substantial overhead by hosting them twice (on the Apprenda share and the particular server that the website will be hosted on). There may also be restrictions on the space your application can take.
In regards to your second question, you can add the delta using the patch builder utility and simply providing the additional files. http://docs.apprenda.com/current/patch-creation