Add a upgrade command method to the Ingress application.

- Adds to specs the case where apps are also updated
- Rename scope calls on Gitlab::UsageData and Clusters::Cluster
- Removes a duplicated spec

All applications except for Jupyter have the same #set_initial_status,
so create a new shared example which we include in all application specs
except for juptyer_spec. Juptyer specs already have specs for it's
version of #set_initial_status

This makes this consistent with :updated. And also avoids a potential
issue where an install errors which means that that the recorded version
won't necessarily reflect the version that is actually installed.

Many changes were also made to tests that expected this to default to
false.

Before this commit updating Prometheus (e.g. adding alerts) made it
"updated" therefore not installed.

Fix up VERSION for each of the applications
* There is no 0.0.1 helm version for jupyterhub. Use the latest version instead
* `:nginx` is not a valid chart version. Lock the ingress application GitLab installs to the latest chart version.
* Use the latest gitlab-runner chart to prevent GitLab installing older versions when users have been installing the lastest version

Always install from the VERSION and not the database `version` column.
This should fix cases like https://gitlab.com/gitlab-org/gitlab-ee/issues/6795 in
the instances where an install command failed previously, which locked the version
in the database to an older version.

Also, ensure that the version column is updated to the version we are
installing.

Add specs to show how previously failed appplications will be handled when the helm installation is run again

Add changelog entry

This reverts merge request !20801

This is refactoring in the lead up to passing mutual TLS certs for helm applications. As such we expect all applications to need config files so we can remove the logic about which applications need and do not need this (ie `#config_map?`).

(#42643)