Follow certificates managed by the companion with a dot file

[buchdag]

As discussed in #465, this PR should fix the remaining issues with hybrid configurations (certs obtained through the companion stored and used along certs obtained another way).

[...] include a dot file next to the certs handled by the companion during creation / renewal (most importantly before the symlink cleanup function). Then the symlink cleanup function check for the presence of this dot file. If it's not there, those files are not handled by the companion, don't touch the symlinks.

@ejbp any thought before merging this ?

[ejbp]

@buchdag It looks very nice. I've nothing further to add. Thanks for the update 👍