That would be great. Currently I'm using a 2 calls process as:

linuxdeploy --appdir AppDir \                                               
            --plugin python                                                 
linuxdeploy --appdir AppDir \                                                
            -i python.png              
            -d python.desktop \                                          
            -e exe \                                   
            --custom-apprun AppRun \                       
            --output appimage

But actually I could even use a 3rd call, where the plugin is run again just before generating the AppImage.

In your case, a single call might be sufficient already, though. But yes, this would be useful.

In my case exe is built by the plugin. If I pack it in a single call it says: exe not found. Also the dependencies of extension modules (#77), built by the plugin as well, are not found at the 1st call. Is there an option to prioritise the plugin?

Your plugin should not depend on subsequent runs of linuxdeploy I guess, or maybe call it automatically then. But it's probably preferrable to use C++ with liblinuxdeploy for it then. I don't know how plugin stages could work around that. Especially since I already mentioned in your tracker that it's preferable for your plugin to use a different prefix.

Anyway, plugin stages are definitely planned.