Update documentation of deployNew.sh

There are some places in the documentation need updating after we changed deployNew.sh to stop reading from `scripts/templates`. We can refer to the script help text and give correct examples.

This includes the deployment guide, the deployment improvements documentation, the release process, the system tests documentation.

The help text in DeployNewInstance also does not explain the ability to pass an instance properties file as the configuration directory in order to read that file and the directory around it, as explained in `docs/deployment/deploy-with-cdk.md`. That article could also be clearer that it will still read the file you specified instead of just falling back to the directory around it.

Start with deployNew.sh and the DeployNewInstance help text, then inspect docs/deployment/deploy-with-cdk.md and the deployment guide, deployment improvements, release process, and system tests documentation. Update the examples and explanations to match the script help, including how an instance properties file and its surrounding directory are handled. Done means all named documentation reflects the current behavior and explains that the specified file is still read.

Written by the indexing model from the issue text.