Support config-file retention configuration for Prometheus >=3.11

[rjhenry]

In Prometheus 3.11, percentage-based retention policies were introduced, although only configurable through the configuration file.
The PR also mentions that the flags --storage.tsdb.retention.time and --storage.tsdb.retention.size are deprecated, which was done in October of 2025.

In order to support the percentage retention, the Prometheus role needs to manage storage configuration in the configuration file, so it makes sense to also move the retention time and size flags to the same file.

[rjhenry]

Sorry for the faux-pas of developing on this without a comment on the issue to say I was doing so - I'd written the comment, but not actually submitted it.