Polish code for PineAPPL 1.x

[t7phy]

• Write missing documentation; addressed in Improve and update deprecated documentations #378
• Cleanup code
• Raise code coverage; code coverage is roughly 98% now

[felixhekhorn]

this line

pineappl/docs/cli-reference.md

Line 68 in 6c9e667

This section specifies the `REMAPPING` parameter of `pineappl remap`.

surely is outdated - this may or may not be true also for other pages of the docs folder

[cschwan]

There's probably even more outdated information in that file; ideally we'd get rid of this file entirely and put the information directly into the source code, directly into the documentation of the program parameters and options, where it getting outdated is less likely.

The necessary feature is markdown support in clap, which luckily for us was added this year in version 4.5.28. I'll try to correct and merge the information.