Use string array in ShellRunner

[jvalkeal]

In ShellRunner we should switch from ApplicationArguments to plain String[] as that's only thing we're going to need from boot.

Should create default methods to bridge new methods, deprecate old ones and remove in 3.4.x. This is getting closer to remove all boot classes from core package.

[jvalkeal]

Previous commit broke something with exit codes as e2e tests started to fail.