Hi Holger,
I generally do not recommend modifying the JSP or other files included in the war as it makes updates to PWM difficult to apply.
I recommend using javascript to make any modifications required; you can embed javascript that runs on all pages using the setting ' Settings ⇨ User Interface ⇨ Look & Feel ⇨ Embedded JavaScript'. This way your changes will be part of the configuration file and remain applied after an upgrade. You can use html attributes on the page to detect what jsp is loaded.
If you must modify files inside the container, then the method I would use would be to clone the git repo, make your changes in files outside the repo and then copy them into your local repo and do a build. This way the docker image could be updated by updating the local repo and recopying your modified files, and then making a new image locally.
Cheers,
-Jason