Store OTP secret key in secrets.yml

## What does this MR do?

Migrate the value of `.secret` to `config/secrets.yml` if present, so that `.secret` can be rotated without preventing all users with 2FA from logging in. (On a clean setup, generate different keys for each.)

## Are there points in the code the reviewer needs to double check?

I'm not sure we actually need `.secret` at all after this, but it seems safer not to touch it.

## Why was this MR needed?

We have some DB encryption keys in `config/secrets.yml`, and one in `.secret`. They should all be in the same place.

## What are the relevant issue numbers?

#3963, which isn't closed until I make the relevant changes in Omnibus too.

## Does this MR meet the acceptance criteria?

- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- [x] [Documentation created/updated](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/development/doc_styleguide.md)
- ~~API support added~~
- Tests
  - [x] Added for this feature/bug
  - [x] All builds are passing
- [x] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [x] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5274