Fix issues with cider-auto-mode

[yuhan0]

The first two commits fix the cider-mode disabling behavior and performance issues mentioned in #3346.
The latter ones introduce a technically breaking change by changing the default setting of cider-auto-mode, and rewording the getting started section of the user manual to something hopefully less misleading and more beginner-friendly.

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[yuhan0]

Sorry for the noisy commits, I'm not sure why these warnings only show up in the CI and not when I run eldev lint / test locally.

[bbatsov]

@yuhan0 Let's pull the change to the default to a separate PR as that's a breaking change likely to affect a lot of users and I want to discuss the implications better.

Generally, I'm worried that a lot of people will be surprised that cider-mode doesn't get enabled automatically. I've gotten a lot of flak in the past for such changes, so I try to be extra careful with them. :-)

[yuhan0]

Ok, I've rebased the non-breaking commits and added on the extra changes from #3354 (going with the double prompt to kill REPLs after choosing not to reuse them)

[yuhan0]

Updated the PR description so #3346 doesn't get auto-closed, discussion can be continued there :)

[bbatsov]

Thanks!