As the application currently doesn't have the ability to update itself you will have to do it manually. But it can be really easy:
- Extract content of zip file
But this is only possible if you have prepared your environment accordingly.
MiWorkplace is an Eclipse RCP application and therefore uses a folder to store anything about the user state of the application like position and state of the parts of the application (like views), preferences, temporary files, etc.
If nothing is specified this folder will be created in the current directory (which is probably application folder) and will be named workspace.
But as this is an Eclipse RCP application various things can be configured, see Eclipse runtime options.
The data option gives you the ability to specify another location for the workspace folder.
./miworkplace -data /home/mihael/devel/miworkplace-workspace
Now you can update the application just be replacing the application folder as the workspace folder is stored someplace else (and not inside the application folder).