We use the File System repository to hold all of our course resources and then link to the resources via an alias/shortcut. We do this so that we can share a single file amongst several courses and if we need to update the file we just have to update the one instance. It also makes it easy to manage all of the files outside of Moodle.
Up to now we have used Flash videos and to get the videos to work using aliases, I have had to create an alias to all of the files in the folder (.htm, .swf, .css and a .js) for a particular flash video instead of just linking to the .htm file. As it is only four files I have been able to manage this but now we are planning on going to HTML5 videos and there are far to many files in an HTML5 output (from Captivate) to make this realistic.
Does anyone know how to get this to work where you just have to link to the index file in the repository to get an HTML5 video to work? I have allow relative files enabled but it does not seem to make a difference.
On another note...the reason we are moving to HTML5 is because we are finding that Flash is not as well supported as it once was and some of our users have had trouble getting it to play.