The Drupal 6 bootstrap easy debug
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Just as a self reminder, and because I don't fancy too much looking into the Drupal core for debugging, here is a short explanation of how the Drupal 7 bootstrap mechanism works.
First of all, a bootstrap mechanism is a mechanism by which you work progressively your way through the full loading of a system, step by step, starting with the loading of simple elements that will allow you to load more complex elements. The Linux system also has a bootstrap mechanism (as do most OSes).