I’m not sure it’s a good idea. I sometimes program websites that also contain .htaccess files.
I would like to transfer these files to my server, but so far this is disabled by oC itself for security reasons.
The data directory is not in the web root directory, but was created with
<Directory /media/owncloud/data> Options Indexes FollowSymLinks AllowOverride ALL Require all granted </Directory>
in /etc/apache2/apache2.conf to the web server.
As far as I know, there is no danger if I allow the .htaccess upload in the config, or am I missing something here?