Howdy, Mark!
(1) Viewing the server, standalone and network client code together all packaged as one jar. Does this actually happen in industry?
Hum... sometimes yes, but it is likely that these components would be distributed in separated .jar files.
Now, the suncertify.properties file has to always be saved in the application working directory. Let's say that you start the application for the first time. Since the file still doesn't exist, you have to create one, no matter how the application was started, but let's say that the application is started in standalone mode. You create the suncertify.properties file and save the values provided by the user. Then, let's say that the application is started in client mode. The values related to the server (IP address or port number, for instance) do not exist in the .properties file, so no values should be displayed to the user. Then, let's say that the application is now started in standalone mode again. The values provided by the user should already exist, so you show them to the user. The point is, you always use the same file to save the values provided by the user. You can create different properties for it.
Cheers, Roberto Perillo
SCJP, SCWCD, SCJD, SCBCD