Move `markup_reference.rb` into `misc` directory

[okuramasafumi]

Close #1123

[okuramasafumi]

https://github.com/ruby/ruby/blob/master/tool/sync_default_gems.rb#L154 This line in ruby/ruby fails, and I don't know what to do... Could we simply delete that line? I still believe this change worth, but if it's too difficult we need to abandon this PR.

[st0012]

We need to update the line so it copies the file from the new destination instead. I think we may limit disruption if we change things this way:

1. We merge this PR, which will NOT be synced to ruby/ruby because the script will fail. But it should not affect other projects' syncing nor fail core's build
   • @hsbt is my understanding correct?
2. Then we open a PR to ruby/ruby to update the script and manually sync the files