diff --git a/cli-script.php b/cli-script.php
index 07bcad2d0..70cbdbf02 100755
--- a/cli-script.php
+++ b/cli-script.php
@@ -1,11 +1,6 @@
 #!/usr/bin/php5
 <?php
 
-if(isset($_SERVER['HTTP_HOST'])) {
-	echo "cli-script.php can't be run from a web request, you have to run it on the command-line.";
-	die();
-}
-
 /**
  * File similar to main.php designed for command-line scripts
  * 
@@ -15,6 +10,20 @@ if(isset($_SERVER['HTTP_HOST'])) {
  * @subpackage core
  */
 
+/**
+ * Ensure that people can't access this from a web-server
+ */
+if(isset($_SERVER['HTTP_HOST'])) {
+	echo "cli-script.php can't be run from a web request, you have to run it on the command-line.";
+	die();
+}
+
+/**
+ * Identify the cli-script.php file and change to its container directory, so that require_once() works
+ */
+$_SERVER['SCRIPT_FILENAME'] = __FILE__;
+chdir(dirname($_SERVER['SCRIPT_FILENAME']));
+
 /**
  * Process arguments and load them into the $_GET and $_REQUEST arrays
  * For example,
@@ -41,106 +50,23 @@ if(isset($_SERVER['argv'][2])) {
 	$_REQUEST = $_GET;
 }
 
-$_SERVER['SCRIPT_FILENAME'] = __FILE__;
-chdir(dirname($_SERVER['SCRIPT_FILENAME']));
-
 /**
  * Include Sapphire's core code
  */
 require_once("core/Core.php");
 
-header("Content-type: text/html; charset=\"utf-8\"");
-if(function_exists('mb_http_output')) {
-	mb_http_output('UTF-8');
-	mb_internal_encoding('UTF-8');
-}
-
-// figure out the server configuration
-if( preg_match( '/(test\.totallydigital\.co\.nz|dev\.totallydigital\.co\.nz\/test)(.*)/', $_SERVER['SCRIPT_FILENAME'], $nameMatch ) ) {
-	$_SERVER['SCRIPT_NAME'] = $nameMatch[2];
-	$_SERVER['HTTP_HOST'] = $nameMatch[1];
-	$envType = 'test';
-} elseif( preg_match( '/dev\.totallydigital\.co\.nz(.*)/', $_SERVER['SCRIPT_FILENAME'], $nameMatch ) ) {
-	$_SERVER['SCRIPT_NAME'] = $nameMatch[1];
-	$envType = 'dev';
-} elseif( preg_match( '/\/sites\/[^\/]+\/www(.*)/', $_SERVER['SCRIPT_FILENAME'], $nameMatch ) ) {
-	$_SERVER['SCRIPT_NAME'] = $nameMatch[1];	
-	$envType = 'live';
-} elseif( preg_match( '/\/sites\/[^\/]+(.*)/', $_SERVER['SCRIPT_FILENAME'], $nameMatch ) ) {
-	$_SERVER['SCRIPT_NAME'] = $nameMatch[1];
-} elseif(isset($_SERVER['SCRIPT_NAME'])) {
-	$envType = 'live';
-} else {
-	echo "Error: could not determine server configuration {$_SERVER['SCRIPT_FILENAME']}\n";
-	exit();	
-}
-
-// set request method (doesn't allow POST through cli)
-$_SERVER['REQUEST_METHOD'] = "GET";	
-
-if($_REQUEST && get_magic_quotes_gpc()) {
-	stripslashes_recursively($_REQUEST);
-}
-
-if(isset($_REQUEST['trace'])) apd_set_pprof_trace();
-
-require_once("core/ManifestBuilder.php");
-require_once("core/ClassInfo.php");
-require_once('core/Object.php');
-require_once('core/control/Director.php');
-require_once('filesystem/Filesystem.php');
-require_once("core/Session.php");
-
-Session::start();
-
-$envFiles = array('../_ss_environment.php', '../../_ss_environment.php', '../../../_ss_environment.php');
-foreach($envFiles as $envFile) {
-	if(file_exists($envFile)) {
-		include($envFile);
-		break;
-	}
-}
-
-// Find the URL of this script
-if(isset($_FILE_TO_URL_MAPPING)) {
-	$fullPath = $testPath = $_SERVER['SCRIPT_FILENAME'];
-	while($testPath && $testPath != "/") {
-		if(isset($_FILE_TO_URL_MAPPING[$testPath])) {
-			$url = $_FILE_TO_URL_MAPPING[$testPath] . substr($fullPath,strlen($testPath));
-			$_SERVER['HTTP_HOST'] = parse_url($url, PHP_URL_HOST);
-			$_SERVER['SCRIPT_NAME'] = parse_url($url, PHP_URL_PATH);
-			$_SERVER['REQUEST_PORT'] = parse_url($url, PHP_URL_PORT);
-			break;
-		}
-		$testPath = dirname($testPath);
-	}
-}
-
-
-if(ManifestBuilder::staleManifest()){
-	ManifestBuilder::compileManifest();
-}		
-
-require_once(MANIFEST_FILE);
-
-if(isset($_GET['debugmanifest'])) Debug::show(file_get_contents(MANIFEST_FILE));
-
-//if(!isset(Director::$environment_type) && $envType) Director::set_environment_type($envType);
-
-// Load error handlers
-Debug::loadErrorHandlers();
+// We don't have a session in cli-script, but this prevents errors
+$_SESSION = null;
 
 // Connect to database
 require_once("core/model/DB.php");
-
 DB::connect($databaseConfig);
 
-
-// Get the request URL
+// Get the request URL from the querystring arguments
 $url = $_SERVER['argv'][1];
-$_SERVER['REQUEST_URI'] = "/$url";
+$_SERVER['REQUEST_URI'] = BASE_URL . '/' . $url;
 
-// Direct away - this is the "main" function, that hands control to the apporopriate controllerx
+// Direct away - this is the "main" function, that hands control to the apporopriate controller
 Director::direct($url);
 
 ?>
diff --git a/core/Core.php b/core/Core.php
index 2d5c73ad3..8df6f116b 100755
--- a/core/Core.php
+++ b/core/Core.php
@@ -1,11 +1,91 @@
 <?php
 /**
- * This file contains several methods that control the core behaviour of Sapphire.
+ * This file is the Sapphire bootstrap.  It will get your environment ready to call Director::direct().
  *
+ * It takes care of:
+ *  - Including _ss_environment.php
+ *  - Normalisation of $_SERVER values
+ *  - Initialisation of TEMP_FOLDER, BASE_URL, BASE_PATH, and other SilverStripe defines
+ *  - Checking of PHP memory limit
+ *  - Including all the files needed to get the manifest built
+ *  - Building and including the manifest
+ * 
+ * @todo This file currently contains a lot of bits and pieces, and its various responsibilities should probably be
+ * moved into different subsystems.
+ * @todo A lot of this stuff is very order-independent; for example, the require_once calls have to happen after the defines.'
+ * This could be decoupled.
  * @package sapphire
  * @subpackage core
  */
 
+///////////////////////////////////////////////////////////////////////////////
+// ENVIRONMENT CONFIG
+
+/**
+ * Include _ss_environment.php files
+ */
+$envFiles = array('../_ss_environment.php', '../../_ss_environment.php', '../../../_ss_environment.php');
+foreach($envFiles as $envFile) {
+	if(file_exists($envFile)) {
+		include($envFile);
+		break;
+	}
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// GLOBALS AND DEFINE SETTING
+
+/**
+ * A blank HTTP_HOST value is used to detect command-line execution.
+ * We update the $_SERVER variable to contain data consistent with the rest of the application.
+ */
+if(!isset($_SERVER['HTTP_HOST'])) {
+	// HTTP_HOST, REQUEST_PORT, SCRIPT_NAME, and PHP_SELF
+	if(isset($_FILE_TO_URL_MAPPING)) {
+		$fullPath = $testPath = $_SERVER['SCRIPT_FILENAME'];
+		while($testPath && $testPath != "/") {
+			if(isset($_FILE_TO_URL_MAPPING[$testPath])) {
+				$url = $_FILE_TO_URL_MAPPING[$testPath] . substr($fullPath,strlen($testPath));
+				$_SERVER['HTTP_HOST'] = parse_url($url, PHP_URL_HOST);
+				$_SERVER['SCRIPT_NAME'] = $_SERVER['PHP_SELF'] = parse_url($url, PHP_URL_PATH);
+				$_SERVER['REQUEST_PORT'] = parse_url($url, PHP_URL_PORT);
+			    break;
+			}
+			$testPath = dirname($testPath);
+		}
+	}
+	
+	// Everything else
+	$serverDefaults = array(
+		'SERVER_PROTOCOL' => 'HTTP/1.1',
+		'HTTP_ACCEPT' => 'text/plain;q=0.5',
+		'HTTP_ACCEPT_LANGUAGE' => '*;q=0.5',
+		'HTTP_ACCEPT_ENCODING' => '',
+		'HTTP_ACCEPT_CHARSET' => 'ISO-8859-1;q=0.5',
+		'SERVER_SIGNATURE' => 'Command-line PHP/' . phpversion(),
+		'SERVER_SOFTWARE' => 'PHP/' . phpversion(),
+		'SERVER_ADDR' => '127.0.0.1',
+		'REMOTE_ADDR' => '127.0.0.1',
+		'REQUEST_METHOD' => 'GET',
+	);
+	
+	$_SERVER = array_merge($serverDefaults, $_SERVER);
+	
+/**
+ * If we have an HTTP_HOST value, then we're being called from the webserver and there are some things that
+ * need checking
+ */
+} else {
+	/**
+	 * Fix magic quotes setting
+	 */
+	if (get_magic_quotes_gpc()) {
+		if($_REQUEST) stripslashes_recursively($_REQUEST);
+		if($_GET) stripslashes_recursively($_GET);
+		if($_POST) stripslashes_recursively($_POST);
+	}
+}
+
 /**
  * Define system paths
  */
@@ -38,6 +118,69 @@ define('PR_HIGH',100);
 define('PR_MEDIUM',50);
 define('PR_LOW',10);
 
+/**
+ * Ensure we have enough memory
+ */
+$memString = ini_get("memory_limit");
+switch(strtolower(substr($memString, -1))) {
+case "k":
+	$memory = round(substr($memString, 0, -1)*1024);
+	break;
+case "m":
+	$memory = round(substr($memString, 0, -1)*1024*1024);
+	break;
+case "g":
+	$memory = round(substr($memString, 0, -1)*1024*1024*1024);
+	break;
+default:
+	$memory = round($memString);
+}
+
+// Check we have at least 32M
+if ($memory < (32 * 1024 * 1024)) {
+	// Increase memory limit
+	ini_set('memory_limit', '32M');
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// INCLUDES
+
+require_once("core/ManifestBuilder.php");
+require_once("core/ClassInfo.php");
+require_once('core/Object.php');
+require_once('core/control/Director.php');
+require_once('filesystem/Filesystem.php');
+require_once("core/Session.php");
+
+///////////////////////////////////////////////////////////////////////////////
+// MANIFEST
+
+/**
+ * Build the manifest
+ */
+if(ManifestBuilder::staleManifest()){
+	ManifestBuilder::compileManifest();
+}		
+
+require_once(MANIFEST_FILE);
+
+/**
+ * ?debugmanifest=1 hook
+ */
+if(isset($_GET['debugmanifest'])) Debug::show(file_get_contents(MANIFEST_FILE));
+
+
+///////////////////////////////////////////////////////////////////////////////
+// POST-MANIFEST COMMANDS
+
+/**
+ * Load error handlers
+ */
+Debug::loadErrorHandlers();
+
+///////////////////////////////////////////////////////////////////////////////
+// HELPER FUNCTIONS
+
 /**
  * Returns the temporary folder that sapphire/silverstripe should use for its cache files
  * This is loaded into the TEMP_FOLDER define on start up
diff --git a/core/control/Director.php b/core/control/Director.php
index 4b7dece0e..0f17e8018 100644
--- a/core/control/Director.php
+++ b/core/control/Director.php
@@ -276,7 +276,8 @@ class Director {
 
 	 	if(substr($url,0,4) != "http") {
 	 		if($url[0] != "/") $url = Director::baseURL()  . $url;
-			$url = self::protocolAndHost() . $url;
+			// Sometimes baseURL() can return a full URL instead of just a path
+			if(substr($url,0,4) != "http") $url = self::protocolAndHost() . $url;
 		}
 
 		return $url;
@@ -289,7 +290,7 @@ class Director {
 	 */
 	static function protocolAndHost() {
 		if(self::$alternateBaseURL) {
-			if(preg_match('/^(http[^:]*:\/\/[^\/]+)\//', self::$alternateBaseURL, $matches)) {
+			if(preg_match('/^(http[^:]*:\/\/[^\/]+)(\/|$)/', self::$alternateBaseURL, $matches)) {
 				return $matches[1];
 			}
 		}
diff --git a/main.php b/main.php
index d866320ad..adb7f78a4 100644
--- a/main.php
+++ b/main.php
@@ -35,16 +35,6 @@
  * @see Director::direct()
  */
 
-/**
- * Include _ss_environment.php file
- */
-$envFiles = array('../_ss_environment.php', '../../_ss_environment.php', '../../../_ss_environment.php');
-foreach ($envFiles as $envFile) {
-        if (@file_exists($envFile)) {
-                include($envFile);
-                break;
-        }
-}
 
 /**
  * Include Sapphire's core code
@@ -57,44 +47,6 @@ if (function_exists('mb_http_output')) {
 	mb_internal_encoding('UTF-8');
 }
 
-if (get_magic_quotes_gpc()) {
-	if($_REQUEST) stripslashes_recursively($_REQUEST);
-	if($_GET) stripslashes_recursively($_GET);
-	if($_POST) stripslashes_recursively($_POST);
-}
-if (isset($_REQUEST['trace'])) {
-	apd_set_pprof_trace();
-}
-
-// Ensure we have enough memory
-$memString = ini_get("memory_limit");
-switch(strtolower(substr($memString, -1))) {
-case "k":
-	$memory = round(substr($memString, 0, -1)*1024);
-	break;
-case "m":
-	$memory = round(substr($memString, 0, -1)*1024*1024);
-	break;
-case "g":
-	$memory = round(substr($memString, 0, -1)*1024*1024*1024);
-	break;
-default:
-	$memory = round($memString);
-}
-
-// Check we have at least 32M
-if ($memory < (32 * 1024 * 1024)) {
-	// Increase memory limit
-	ini_set('memory_limit', '32M');
-}
-
-
-require_once("core/ClassInfo.php");
-require_once('core/Object.php');
-require_once('core/control/Director.php');
-require_once('filesystem/Filesystem.php');
-require_once("core/Session.php");
-
 // If this is a dev site, enable php error reporting
 // This is necessary to force developers to acknowledge and fix
 // notice level errors (you can override this directive in your _config.php)
@@ -104,6 +56,7 @@ if (Director::isDev()) {
 
 Session::start();
 
+// Apache rewrite rules use this
 if (isset($_GET['url'])) {
 	$url = $_GET['url'];
 	
@@ -114,23 +67,16 @@ if (isset($_GET['url'])) {
 	if ($_GET) $_REQUEST = array_merge((array)$_REQUEST, (array)$_GET);
 }
 
-require_once("core/ManifestBuilder.php");
-if (ManifestBuilder::staleManifest()) {
-	ManifestBuilder::compileManifest();
+// Fix glitches in URL generation
+if (substr($url, 0, strlen(BASE_URL)) == BASE_URL) $url = substr($url, strlen(BASE_URL));
+
+
+if (isset($_GET['debug_profile'])) {
+	Profiler::init();
+	Profiler::mark('all_execution');
+	Profiler::mark('main.php init');
 }
 
-require_once(MANIFEST_FILE);
-
-if (isset($_GET['debugmanifest'])) Debug::show(file_get_contents(MANIFEST_FILE));
-
-if (isset($_GET['debug_profile'])) Profiler::init();
-if (isset($_GET['debug_profile'])) Profiler::mark('all_execution');
-
-if (isset($_GET['debug_profile'])) Profiler::mark('main.php init');
-
-// Load error handlers
-Debug::loadErrorHandlers();
-
 // Connect to database
 require_once("core/model/DB.php");
 
@@ -138,12 +84,9 @@ if (isset($_GET['debug_profile'])) Profiler::mark('DB::connect');
 DB::connect($databaseConfig);
 if (isset($_GET['debug_profile'])) Profiler::unmark('DB::connect');
 
-
-// Get the request URL
-if (substr($url, 0, strlen(BASE_URL)) == BASE_URL) $url = substr($url, strlen(BASE_URL));
+if (isset($_GET['debug_profile'])) Profiler::unmark('main.php init');
 
 // Direct away - this is the "main" function, that hands control to the appropriate controller
-if (isset($_GET['debug_profile'])) Profiler::unmark('main.php init');
 Director::direct($url);
 
 if (isset($_GET['debug_profile'])) {
diff --git a/tests/control/DirectorTest.php b/tests/control/DirectorTest.php
index 7202726df..daaea2fa0 100644
--- a/tests/control/DirectorTest.php
+++ b/tests/control/DirectorTest.php
@@ -26,25 +26,25 @@ class DirectorTest extends SapphireTest {
 		
 		unlink($tempFilePath);
 	}
-	/*
+
 	public function testAlternativeBaseURL() {
-		// relative base URLs
-		Director::setBaseURL('/relativebase');
-		$this->assertEquals(Director::baseURL(), '/relativebase');
-		$this->assertEquals(Director::absoluteBaseURL(), BASE_URL . '/relativebase');
-		$this->assertEquals(Director::absoluteURL('subfolder'), $origBaseURL . '/relativebase/subfolder');
-		
-		// absolute base URLs
-		Director::setBaseURL('http://www.example.org');
-		$this->assertEquals(Director::baseURL(), 'http://www.example.org');
-		$this->assertEquals(Director::absoluteBaseURL(), 'http://www.example.org');
-		$this->assertEquals(Director::absoluteURL('subfolder'), 'http://www.example.org/subfolder');
-		
+		// relative base URLs - you should end them in a /
+		Director::setBaseURL('/relativebase/');
+		$this->assertEquals('/relativebase/', Director::baseURL());
+		$this->assertEquals(Director::protocolAndHost() . '/relativebase/', Director::absoluteBaseURL());
+		$this->assertEquals(Director::protocolAndHost() . '/relativebase/subfolder/test', Director::absoluteURL('subfolder/test'));
+
+		// absolute base URLs - you should end them in a /
+		Director::setBaseURL('http://www.example.org/');
+		$this->assertEquals('http://www.example.org/', Director::baseURL());
+		$this->assertEquals('http://www.example.org/', Director::absoluteBaseURL());
+		$this->assertEquals('http://www.example.org/subfolder/test', Director::absoluteURL('subfolder/test'));
+
+		// Setting it to false restores functionality
 		Director::setBaseURL(false);
-		$this->assertEquals(Director::baseURL(), BASE_URL);
-		$this->assertEquals(Director::absoluteBaseURL(BASE_URL), BASE_URL);
-		$this->assertEquals(Director::absoluteURL('subfolder'), BASE_URL . '/subfolder');
+		$this->assertEquals(BASE_URL.'/', Director::baseURL());
+		$this->assertEquals(Director::protocolAndHost().BASE_URL.'/', Director::absoluteBaseURL(BASE_URL));
+		$this->assertEquals(Director::protocolAndHost().BASE_URL . '/subfolder/test', Director::absoluteURL('subfolder/test'));
 	}
-	*/
 }
 ?>
\ No newline at end of file