Replace base R message/warning/stop with {cli}

[jamesmbaazam]

Description

This PR closes #546.

This PR replaces the use of base condition signalling with those provided by {cli} as it offers more powerful features such as the ability to display a warning every few hours.

As part of this PR, I've updated the .lintr config file to catch future uses of base messaging. This was really useful in the refactoring exercise as it caught all occurrences. There were some false positives in the regional_epinow.R, so I embraced them in #nolint undesirable_function_linter tags to counter the configs I've set up.

Initial submission checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have tested my changes locally (using devtools::test() and devtools::check()).
• I have added or updated unit tests where necessary.
• I have updated the documentation if required and rebuilt docs if yes (using devtools::document()).
• I have followed the established coding standards (and checked using lintr::lint_package()).
• I have added a news item linked to this PR.

After the initial Pull Request

• I have reviewed Checks for this PR and addressed any issues as far as I am able.

[seabbs]

This looks great. Like the lintr as the package check and the use of colour highlighting. You have some very unhappy CI which I expect is due to error and warning testing needing to be updated.

[jamesmbaazam]

Sorry, I should have marked this as a draft. Have a few simple fixes then we can try the new changes and see if happy before merging, or we can merge this and apply fancier stuff in another run. {cli} is addictive and I'm trying not to go crazy.

[seabbs]

Have a few simple fixes then we can try the new changes and see if happy before merging

Ha I know I think this and do fancier stuff in a new PR

[seabbs]

Nice. Looks good.