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I'm not sure what file i/o has to do with connecting to a database? Even so, most server-sided scripting languages such as PHP/ASP/Ruby/Perl have the ability to modify files on the file system.
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Well the data is stored as a file somewhere, but when working with a database such as MySQL, you communicate directly with a mysql server. The way the mysql server saves its information is beyond me - but I know it does takes advantage of a B-Tree structure.
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I have never heard anybody complain about Joomla. I guess it is really advanced and user-friendly.
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I have some complaints against Joomla! but it mainly relates to the editors available and the fact that they change my HTML code. Other than that Joomla! is great.
@Xav: I agree with that.
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I suppose everything has its flaws.
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