Everything else is finally simply details -- important details, but variants on that theme. index.php is the control, the menu method determins what the "existing page" is, and plenty of events get fired along the way of building that page. Plugin modules can hook in to those occasions and change the workflow/supply additional tips/etc. That is also a part of the reason a lot of Drupal resources focus on making modules. Without modules, Drupal does not really DO something other than say, 'Some one asked for a page! Does it exist? No? OK, I'll serve up a 404.'

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