Use the latest jQuery with your Drupal theme

template.php

<?php
function {theme_name}_preprocess(&$vars, $hook) {
		 if (arg(0) != 'admin' && $hook == "page") {
			// Get an array of all JavaScripts that have been added
			$javascript = drupal_add_js(NULL, NULL, 'header');
			
			// Remove the original jQuery library and Drupal's JS include
			unset($javascript['core']['misc/jquery.js']);
			unset($javascript['core']['misc/drupal.js']);
		
			// Add in our new jQuery library and Drupal's JS include
			// We do it this way to keep the includes in the same order
			$core = array(
				//Alternative jQuery
				drupal_get_path('theme', '{theme_name}').'/js/libs/jquery-1.5.1.min.js' => array(
					'cache' => TRUE, 
					'defer' => FALSE,
				),
				'misc/drupal.js' => array(
					'cache' => TRUE, 
					'defer' => FALSE,
				)
			);
		
			// Merge back into the array of core JavaScripts 
			$javascript['core'] = array_merge($javascript['core'], $core);

			// Rerender the block of JavaScripts
			$vars['scripts'] = drupal_get_js(NULL, $javascript);
		}
}
?>

Instead of removing jQuery and Drupal.js, why not instead just add another jQuery:

$core = array(
//Alternative jQuery
drupal_get_path('theme', 'linamar').'/js/libs/jquery-1.5.1.noconflict.min.js' => array(
'cache' => TRUE,
'defer' => FALSE,
)...);

Where jquery-1.5.1.noconflict.min.js = [minified jQuery source] + var $j = jQuery.noConflict();

Not the greatest solution, but it will not bust things on the front end that rely on jQuery 1.2.6

Also, that should be jquery 1.5.2 should it not?

Adding a second jQuery in another namespace was suggested, but I don't like the thought of loading jQuery twice - it's small but not that small.

I'm not sure, 1.5.1 is what came with the HTML5 Boilerplate.

My goal is to have the frontend completely independent of Drupal styles and scripts.

My goal is to have the frontend completely independent of Drupal styles and scripts.

A lofty goal, but there are lots of modules that use javascript on the front end...

Which admin menu are you using?

I was using a module called Administration, but now I'm using a module called Toolbars

wow Toolbar is really bad - switching to SimpleMenu. Working fine so far!

totally using this on http://i.seanja.com so I can use a lightbox plugin to show the images full size

Hmmm... it doesn't really work with compression turned on...

Does it include it? Does it include Drupal's jQuery instead?

I think it might be, I am going to try it out again when I get home to see what it is actually doing.