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For option 1, I understand that the use of PHP and MySQL are the standard of working in the University (also that there are not much ports open for apps and HTTP port is open), but when writing a new file I would imagine at least a script/program (C, C++, Java, Python, Perl, Haskell, Erlang, Bash... any option is good) that reads the new files; creates the bundle information and posts it on MySQL. I don't like the idea of having a literal file loader through PHP a lot of security issues can arise. And as the developers we should have access to the server that hosts the files.
Actually there could be a cron that pulls the git repo and we can add a hook that runs the program after every pull.
Check the wiki-entry: https://github.com/GIDAIbero/GIDAFileUpdater/wiki/ProjectStructure
Option 2 should be up on... 3 or 4 days more... let's start discussing option 1
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