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I'm looking into template files for theming purposes, and often at the beginning of the file there is a // $Id$ mark.

Could you explain me what it mean, and what the purpose of it is?

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It is a placeholder, that is automatically replaced by CVS and then contains information about CVS version, author and so on of the file. For more information, see http://badgertronics.com/writings/cvs/keywords.html.

Since Drupal.org recently switched to Git as the version control system, this tag is now completely irrelevant so it can and should be removed. In fact, it has been removed automatically during the CVS -> Git migration for all modules on drupal.org

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