diff --git a/lib/pkp/classes/cliTool/CliTool.inc.php b/lib/pkp/classes/cliTool/CliTool.inc.php
--- a/lib/pkp/classes/cliTool/CliTool.inc.php
+++ b/lib/pkp/classes/cliTool/CliTool.inc.php
@@ -19,15 +19,16 @@
  *  to bootstrap and route tool requests.
  */
 
-// $Id$
-
-
 /** Initialization code */
-define('PWD', getcwd());
-chdir(dirname(INDEX_FILE_LOCATION)); /* Change to base directory */
+define('INDEX_FILE_LOCATION', getcwd() . '/index.php');
+if (!file_exists(getcwd() . '/config.TEMPLATE.inc.php')) {
+	die("This script must be executed from the installation base directory.\n");
+}
+
 if (!defined('STDIN')) {
 	define('STDIN', fopen('php://stdin','r'));
 }
+
 define('SESSION_DISABLE_INIT', 1);
 require('./lib/pkp/includes/bootstrap.inc.php');
 
diff --git a/lib/pkp/classes/cliTool/XmlToSqlTool.inc.php b/lib/pkp/classes/cliTool/XmlToSqlTool.inc.php
--- a/lib/pkp/classes/cliTool/XmlToSqlTool.inc.php
+++ b/lib/pkp/classes/cliTool/XmlToSqlTool.inc.php
@@ -54,16 +54,9 @@ class XmlToSqlTool extends CommandLineTool {
 
 		$this->command = $this->argv[$argOffset];
 
-		$file = isset($this->argv[$argOffset+1]) ? $this->argv[$argOffset+1] : DATABASE_XML_FILE;
+		$this->inputFile = isset($this->argv[$argOffset+1]) ? $this->argv[$argOffset+1] : DATABASE_XML_FILE;
 
-		if (!file_exists($file) && !file_exists(($file2 = PWD . '/' . $file))) {
-			printf("Input file \"%s\" does not exist!\n", $file);
-			exit(1);
-		}
-
-		$this->inputFile = isset($file2) ? $file2 : $file;
-
-		$this->outputFile = isset($this->argv[$argOffset+2]) ? PWD . '/' . $this->argv[$argOffset+2] : null;
+		$this->outputFile = isset($this->argv[$argOffset+2]) ? $this->argv[$argOffset+2] : null;
 		if (in_array($this->command, array('save', 'save_upgrade')) && ($this->outputFile == null || (file_exists($this->outputFile) && (is_dir($this->outputFile) || !is_writeable($this->outputFile))) || !is_writable(dirname($this->outputFile)))) {
 			printf("Invalid output file \"%s\"!\n", $this->outputFile);
 			exit(1);
diff --git a/lib/pkp/tests/phpunit.php b/lib/pkp/tests/phpunit.php
--- a/lib/pkp/tests/phpunit.php
+++ b/lib/pkp/tests/phpunit.php
@@ -8,9 +8,10 @@
  */
 // Configure the index file location, assume that pkp-lib is
 // included within a PKP application.
-// FIXME: This doesn't work if lib/pkp is symlinked. realpath($_['SCRIPT_FILENAME'].'/../../index.php') could work but see http://bugs.php.net/bug.php?id=50366
-define('INDEX_FILE_LOCATION', dirname(dirname(dirname(dirname(__FILE__)))).'/index.php');
-chdir(dirname(INDEX_FILE_LOCATION));
+define('INDEX_FILE_LOCATION', getcwd() . '/index.php');
+if (!file_exists(getcwd() . '/config.TEMPLATE.inc.php')) {
+	die("This script must be executed from the installation base directory.\n");
+}
 
 // Configure PKP error handling for tests
 define('DONT_DIE_ON_ERROR', true);
diff --git a/lib/pkp/tools/phpCompat.php b/lib/pkp/tools/phpCompat.php
--- a/lib/pkp/tools/phpCompat.php
+++ b/lib/pkp/tools/phpCompat.php
@@ -40,10 +40,11 @@
  *        for information about detection accuracy.
  */
 
-// $Id$
+define('INDEX_FILE_LOCATION', getcwd() . '/index.php');
+if (!file_exists(getcwd() . '/config.TEMPLATE.inc.php')) {
+	die("This script must be executed from the installation base directory.\n");
+}
 
-// FIXME: This doesn't work if lib/pkp is symlinked. realpath($_['SCRIPT_FILENAME'].'/../../index.php') could work but see http://bugs.php.net/bug.php?id=50366
-define('INDEX_FILE_LOCATION', dirname(dirname(dirname(dirname(__FILE__)))) . '/index.php');
 require_once(dirname(dirname(__FILE__)) . '/classes/cliTool/CliTool.inc.php');
 require_once('PHP/CompatInfo.php');
 
diff --git a/plugins/importexport/native/NativeImportDom.inc.php b/plugins/importexport/native/NativeImportDom.inc.php
--- a/plugins/importexport/native/NativeImportDom.inc.php
+++ b/plugins/importexport/native/NativeImportDom.inc.php
@@ -324,11 +324,6 @@ class NativeImportDom {
 			if (($href = $node->getChildByName('href'))) {
 				$url = $href->getAttribute('src');
 				if ($isCommandLine || NativeImportDom::isAllowedMethod($url)) {
-					if ($isCommandLine && NativeImportDom::isRelativePath($url)) {
-						// The command-line tool does a chdir; we need to prepend the original pathname to relative paths so we're not looking in the wrong place.
-						$url = PWD . '/' . $url;
-					}
-
 					$originalName = basename($url);
 					$newName .= $publicFileManager->getExtension($originalName);
 					if (!$publicFileManager->copyJournalFile($journal->getId(), $url, $newName)) {
@@ -394,11 +389,6 @@ class NativeImportDom {
 			if (($href = $node->getChildByName('href'))) {
 				$url = $href->getAttribute('src');
 				if ($isCommandLine || NativeImportDom::isAllowedMethod($url)) {
-					if ($isCommandLine && NativeImportDom::isRelativePath($url)) {
-						// The command-line tool does a chdir; we need to prepend the original pathname to relative paths so we're not looking in the wrong place.
-						$url = PWD . '/' . $url;
-					}
-
 					$originalName = basename($url);
 					$newName .= $publicFileManager->getExtension($originalName);
 					if (!$publicFileManager->copyJournalFile($journal->getId(), $url, $newName)) {
@@ -996,11 +986,6 @@ class NativeImportDom {
 		if (($href = $node->getChildByName('href'))) {
 			$url = $href->getAttribute('src');
 			if ($isCommandLine || NativeImportDom::isAllowedMethod($url)) {
-				if ($isCommandLine && NativeImportDom::isRelativePath($url)) {
-					// The command-line tool does a chdir; we need to prepend the original pathname to relative paths so we're not looking in the wrong place.
-					$url = PWD . '/' . $url;
-				}
-
 				if (($fileId = $articleFileManager->copyPublicFile($url, $href->getAttribute('mime_type')))===false) {
 					$errors[] = array('plugins.importexport.native.import.error.couldNotCopy', array('url' => $url));
 					return false;
@@ -1050,11 +1035,6 @@ class NativeImportDom {
 			if (($href = $node->getChildByName('href'))) {
 				$url = $href->getAttribute('src');
 				if ($isCommandLine || NativeImportDom::isAllowedMethod($url)) {
-					if ($isCommandLine && NativeImportDom::isRelativePath($url)) {
-						// The command-line tool does a chdir; we need to prepend the original pathname to relative paths so we're not looking in the wrong place.
-						$url = PWD . '/' . $url;
-					}
-
 					if (($fileId = $articleFileManager->copyPublicFile($url, $href->getAttribute('mime_type')))===false) {
 						$errors[] = array('plugins.importexport.native.import.error.couldNotCopy', array('url' => $url));
 						return false;
@@ -1206,11 +1186,6 @@ class NativeImportDom {
 		if (($href = $fileNode->getChildByName('href'))) {
 			$url = $href->getAttribute('src');
 			if ($isCommandLine || NativeImportDom::isAllowedMethod($url)) {
-				if ($isCommandLine && NativeImportDom::isRelativePath($url)) {
-					// The command-line tool does a chdir; we need to prepend the original pathname to relative paths so we're not looking in the wrong place.
-					$url = PWD . '/' . $url;
-				}
-
 				if (($fileId = $articleFileManager->copySuppFile($url, $href->getAttribute('mime_type')))===false) {
 					$errors[] = array('plugins.importexport.native.import.error.couldNotCopy', array('url' => $url));
 					return false;
diff --git a/plugins/importexport/native/NativeImportExportPlugin.inc.php b/plugins/importexport/native/NativeImportExportPlugin.inc.php
--- a/plugins/importexport/native/NativeImportExportPlugin.inc.php
+++ b/plugins/importexport/native/NativeImportExportPlugin.inc.php
@@ -343,10 +343,6 @@ class NativeImportExportPlugin extends ImportExportPlugin {
 		}
 
 		$this->import('NativeImportDom');
-		if ($xmlFile && NativeImportDom::isRelativePath($xmlFile)) {
-			$xmlFile = PWD . '/' . $xmlFile;
-		}
-
 		switch ($command) {
 			case 'import':
 				$userName = array_shift($args);