Apache may sometime crash or stop for many reasons. I had this issue with one of the server where Let’s Encrypt post hook does not start Apache for whatever reasons.
GitLab(9.5) recently introduced GPG commit verification. On Ubuntu 16.04.x gpg2 is installed and can be used instead of gpg which is in the latest docs published for GPG with 9.5 release.
I personally did not find any app or settings which could easily do this, though this is not an app or gui, but its the simplest and easiest way at least for me.
By default NextCloud has index.php in the urls, it’s not a show stopper at all but it’s good to have nice clean urls when sharing.