Fix disabled value for `--prune.*` flags (#4165)

* Changes:
* Proceeded to check if other h, r, t or c flags for 'before' and 'older' are set before returning from the default state of --prune
Concern:
* Does the 'disabled' value for '--prune=' need to be updated if the '--prune.*' flags are set but the '--prune=' flag is not?

* Modify mode.Initialised only when it is changed

* Updated layout for --prune=*

* save

* save

Co-authored-by: alex.sharov <AskAlexSharov@gmail.com>