When modifying files, I am getting permission denied
The shell you get from adb shell doesn't run with special privileges, so you can't read or write files that you wouldn't be able to with a normal app. If you want to access apps' private data files, you still need to get root permission in the usual way, and use su from the shell.

It's not possible to bypass the permissions system. If you want to access inaccessible files, you need to root the device, then use a root app to access them.