> --git a/pts-core/library/pts-functions.php b/pts-core/library/pts-functions.php
index 539ec25..729d09b 100644
--- a/pts-core/library/pts-functions.php
+++ b/pts-core/library/pts-functions.php
@@ -57,7 +57,6 @@ require(PTS_LIBRARY_PATH . "pts-functions_client.php");

 // Load Main Functions
 require(PTS_LIBRARY_PATH . "pts-functions_io.php");
-require(PTS_LIBRARY_PATH . "pts-functions_shell.php");
 require(PTS_LIBRARY_PATH . "pts-functions_system.php");
 require(PTS_LIBRARY_PATH . "pts-functions_global.php");
 require(PTS_LIBRARY_PATH . "pts-functions_tests.php");
diff --git a/pts-core/library/pts-functions_basic.php b/pts-core/library/pts-functions_basic.php
index f102df9..98dfd67 100644
--- a/pts-core/library/pts-functions_basic.php
+++ b/pts-core/library/pts-functions_basic.php
@@ -103,4 +103,61 @@ function pts_to_array($var)
     return !is_array($var) ? array($var) : $var;
 }

+function pts_exec($exec, $extra_vars = null)
+{
+    // Same as shell_exec() but with the PTS env variables added in
+    return shell_exec(pts_variables_export_string($extra_vars) . $exec);
+}
+function pts_remove($object, $ignore_files = null, $remove_root_directory = false)
+{
+    if(is_dir($object))
+    {
+        $object = pts_add_trailing_slash($object);
+    }
+
+    foreach(pts_glob($object . "*") as $to_remove)
+    {
+        if(is_file($to_remove))
+        {
+            if(is_array($ignore_files) && in_array(basename($to_remove), $ignore_files))
+            {
+                continue; // Don't remove the file
+            }
+            else
+            {
+                @unlink($to_remove);
+            }
+        }
+        else if(is_dir($to_remove))
+        {
+            pts_remove($to_remove, $ignore_files, true);
+        }
+    }
+
+    if($remove_root_directory && is_dir($object) && count(pts_glob($object . "/*")) == 0)
+    {
+        @rmdir($object);
+    }
+}
+function pts_copy($from, $to)
+{
+    // Copies a file
+    if(!is_file($to) || md5_file($from) != md5_file($to))
+    {
+        copy($from, $to);
+    }
+}
+function pts_rename($from, $to)
+{
+    return rename($from, $to);
+}
+function pts_symlink($from, $to)
+{
+    return @symlink($from, $to);
+}
+function pts_move($from, $to)
+{
+    return rename($from, $to);
+}
+
 ?>
diff --git a/pts-core/library/pts-functions_shell.php b/pts-core/library/pts-functions_shell.php
deleted file mode 100644
index 253004f..0000000
--- a/pts-core/library/pts-functions_shell.php
+++ /dev/null
@@ -1,81 +0,0 @@
-<?php
-
-/*
-    Phoronix Test Suite
-    URLs: http://www.phoronix.com, http://www.phoronix-test-suite.com/
-    Copyright (C) 2008 - 2010, Phoronix Media
-    Copyright (C) 2008 - 2010, Michael Larabel
-    pts-functions_shell.php: Functions for shell (and similar) commands that are abstracted
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-function pts_exec($exec, $extra_vars = null)
-{
-    // Same as shell_exec() but with the PTS env variables added in
-    return shell_exec(pts_variables_export_string($extra_vars) . $exec);
-}
-function pts_remove($object, $ignore_files = null, $remove_root_directory = false)
-{
-    if(is_dir($object))
-    {
-        $object = pts_add_trailing_slash($object);
-    }
-
-    foreach(pts_glob($object . "*") as $to_remove)
-    {
-        if(is_file($to_remove))
-        {
-            if(is_array($ignore_files) && in_array(basename($to_remove), $ignore_files))
-            {
-                continue; // Don't remove the file
-            }
-            else
-            {
-                @unlink($to_remove);
-            }
-        }
-        else if(is_dir($to_remove))
-        {
-            pts_remove($to_remove, $ignore_files, true);
-        }
-    }
-
-    if($remove_root_directory && is_dir($object) && count(pts_glob($object . "/*")) == 0)
-    {
-        @rmdir($object);
-    }
-}
-function pts_copy($from, $to)
-{
-    // Copies a file
-    if(!is_file($to) || md5_file($from) != md5_file($to))
-    {
-        copy($from, $to);
-    }
-}
-function pts_rename($from, $to)
-{
-    return rename($from, $to);
-}
-function pts_symlink($from, $to)
-{
-    return @symlink($from, $to);
-}
-function pts_move($from, $to)
-{
-    return rename($from, $to);
-}
-
-?>
diff --git a/pts-core/library/pts-includes-batch.php b/pts-core/library/pts-includes-batch.php
deleted file mode 100644
index 1ea663f..0000000
--- a/pts-core/library/pts-includes-batch.php
+++ /dev/null
@@ -1,45 +0,0 @@
-<?php
-
-/*
-    Phoronix Test Suite
-    URLs: http://www.phoronix.com, http://www.phoronix-test-suite.com/
-    Copyright (C) 2008 - 2010, Phoronix Media
-    Copyright (C) 2008 - 2010, Michael Larabel
-    pts-includes-batch.php: Functions Needed When Running In Batch Mode
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-function pts_batch_mode_configured()
-{
-    return pts_strings::string_bool(pts_config::read_user_config(P_OPTION_BATCH_CONFIGURED, "FALSE"));
-}
-function pts_batch_prompt_test_identifier()
-{
-    return pts_strings::string_bool(pts_config::read_user_config(P_OPTION_BATCH_PROMPTIDENTIFIER, "TRUE"));
-}
-function pts_batch_prompt_test_description()
-{
-    return pts_strings::string_bool(pts_config::read_user_config(P_OPTION_BATCH_PROMPTDESCRIPTION, "FALSE"));
-}
-function pts_batch_prompt_save_name()
-{
-    return pts_strings::string_bool(pts_config::read_user_config(P_OPTION_BATCH_PROMPTSAVENAME, "FALSE"));
-}
-function pts_batch_run_all_test_options()
-{
-    return pts_strings::string_bool(pts_config::read_user_config(P_OPTION_BATCH_TESTALLOPTIONS, "TRUE"));
-}
-
-?>
diff --git a/pts-core/library/pts-includes-iqc.php b/pts-core/library/pts-includes-iqc.php
deleted file mode 100644
index 3a0555e..0000000
--- a/pts-core/library/pts-includes-iqc.php
+++ /dev/null
@@ -1,58 +0,0 @@
-<?php
-
-/*
-    Phoronix Test Suite
-    URLs: http://www.phoronix.com, http://www.phoronix-test-suite.com/
-    Copyright (C) 2009, Phoronix Media
-    Copyright (C) 2009, Michael Larabel
-    pts-includes-comparisons.php: Functions needed for performing reference comparisons
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-function pts_rgb_gd_color_at(&$img, $x, $y)
-{
-    $rgb = imagecolorat($img, $x, $y);
-
-    // R, G, B
-    return array(($rgb >> 16) & 0xFF, ($rgb >> 8) & 0xFF, $rgb & 0xFF);
-}
-function pts_rgb_int_diff($rgb1, $rgb2)
-{
-    return abs(array_sum($rgb1) - array_sum($rgb2));
-}
-function pts_color_pixel_delta(&$base_img, &$compare_img, &$x, &$y)
-{
-    $color = false; // for now we set to true when it should change, but ultimately should return a color
-
-    $check_points = array(
-    array($x + 1, $y),
-    array($x - 1, $y),
-    array($x, $y + 1),
-    array($x, $y - 1)
-    );
-
-    foreach($check_points as $point_r)
-    {
-        if(pts_rgb_int_diff(pts_rgb_gd_color_at($base_img, $point_r[0], $point_r[1]), pts_rgb_gd_color_at($compare_img, $point_r[0], $point_r[1])) > 12)
-        {
-            $color = array($point_r[0], $point_r[1]);
-            break;
-        }
-    }
-
-    return $color;
-}
-
-?>
diff --git a/pts-core/library/pts-includes-run_setup.php b/pts-core/library/pts-includes-run_setup.php
index b8b9a79..7fa737a 100644
--- a/pts-core/library/pts-includes-run_setup.php
+++ b/pts-core/library/pts-includes-run_setup.php
@@ -59,7 +59,7 @@ function pts_prompt_results_identifier(&$test_run_manager)
         $current_software = array();
     }

-    if(pts_read_assignment("IS_BATCH_MODE") == false || pts_batch_prompt_test_identifier())
+    if(pts_read_assignment("IS_BATCH_MODE") == false || pts_config::read_bool_config(P_OPTION_BATCH_PROMPTIDENTIFIER, "TRUE"))
     {
         if(count($current_identifiers) > 0)
         {
@@ -119,7 +119,7 @@ function pts_prompt_save_file_name(&$test_run_manager, $check_env = true)
         }
     }

-    if(pts_read_assignment("IS_BATCH_MODE") == false || pts_batch_prompt_save_name())
+    if(pts_read_assignment("IS_BATCH_MODE") == false || pts_config::read_bool_config(P_OPTION_BATCH_PROMPTSAVENAME, "FALSE"))
     {
         while(($is_reserved_word = pts_is_run_object($proposed_name)) || empty($proposed_name))
         {
diff --git a/pts-core/library/pts-includes-unit_caching.php b/pts-core/library/pts-includes-unit_caching.php
deleted file mode 100644
index 7fb6167..0000000
--- a/pts-core/library/pts-includes-unit_caching.php
+++ /dev/null
@@ -1,46 +0,0 @@
-<?php
-
-/*
-    Phoronix Test Suite
-    URLs: http://www.phoronix.com, http://www.phoronix-test-suite.com/
-    Copyright (C) 2009, Phoronix Media
-    Copyright (C) 2009, Michael Larabel
-    pts-includes-unit_caching.php: Functions that simply call pts-core functions for building their caches
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program. If not, see <http://www.gnu.org/licenses/>.
-*/
-
-function pts_cache_suite_calls()
-{
-    pts_supported_suites_array();
-    // pts_available_suites_array(); // This is already called within pts_supported_suites_array()
-    pts_suite_name_to_identifier(-1);
-}
-function pts_cache_test_calls()
-{
-    pts_tests::supported_tests();
-    pts_test_name_to_identifier(-1);
-}
-function pts_cache_hardware_calls()
-{
-    pts_hw_string();
-    phodevi::supported_sensors();
-    phodevi::unsupported_sensors();
-}
-function pts_cache_software_calls()
-{
-    pts_sw_string();
-}
-
-?>
diff --git a/pts-core/objects/pts_client.php b/pts-core/objects/pts_client.php
index ebe2f6c..4e603c4 100644
--- a/pts-core/objects/pts_client.php
+++ b/pts-core/objects/pts_client.php
@@ -425,6 +425,26 @@ class pts_client
             }
         }
     }
+    public static function cache_suite_calls()
+    {
+        pts_supported_suites_array();
+        pts_suite_name_to_identifier(-1);
+    }
+    public static function cache_test_calls()
+    {
+        pts_tests::supported_tests();
+        pts_test_name_to_identifier(-1);
+    }
+    public static function cache_hardware_calls()
+    {
+        pts_hw_string();
+        phodevi::supported_sensors();
+        phodevi::unsupported_sensors();
+    }
+    public static function cache_software_calls()
+    {
+        pts_sw_string();
+    }
 }

 ?>
diff --git a/pts-core/objects/pts_config.php b/pts-core/objects/pts_config.php
index 8da3ef3..3f14ce1 100644
--- a/pts-core/objects/pts_config.php
+++ b/pts-core/objects/pts_config.php
@@ -150,6 +150,11 @@ class pts_config

         return !empty($read_value) ? $read_value : $predefined_value;
     }
+    public static function read_bool_config($xml_pointer, $predefined_value = false, &$tandem_xml = null)
+    {
+        $value = read_user_config($xml_pointer, $predefined_value, $tandem_xml);
+        return pts_strings::string_bool($value);
+    }
     public static function read_graph_config($xml_pointer, $predefined_value = false, &$tandem_xml = null)
     {
         // Generic call for reading a config file
diff --git a/pts-core/objects/pts_image.php b/pts-core/objects/pts_image.php
index c815807..8857cae 100644
--- a/pts-core/objects/pts_image.php
+++ b/pts-core/objects/pts_image.php
@@ -77,6 +77,39 @@ class pts_image

         return $img;
     }
+    public static function rgb_gd_color_at(&$img, $x, $y)
+    {
+        $rgb = imagecolorat($img, $x, $y);
+
+        // R, G, B
+        return array(($rgb >> 16) & 0xFF, ($rgb >> 8) & 0xFF, $rgb & 0xFF);
+    }
+    public static function rgb_int_diff($rgb1, $rgb2)
+    {
+        return abs(array_sum($rgb1) - array_sum($rgb2));
+    }
+    public static function color_pixel_delta(&$base_img, &$compare_img, &$x, &$y)
+    {
+        $color = false; // for now we set to true when it should change, but ultimately should return a color
+
+        $check_points = array(
+        array($x + 1, $y),
+        array($x - 1, $y),
+        array($x, $y + 1),
+        array($x, $y - 1)
+        );
+
+        foreach($check_points as $point_r)
+        {
+            if(pts_image::rgb_int_diff(pts_image::rgb_gd_color_at($base_img, $point_r[0], $point_r[1]), pts_image::rgb_gd_color_at($compare_img, $point_r[0], $point_r[1])) > 12)
+            {
+                $color = array($point_r[0], $point_r[1]);
+                break;
+            }
+        }
+
+        return $color;
+    }
 }

 ?>
diff --git a/pts-core/options/analyze_image_delta.php b/pts-core/options/analyze_image_delta.php
index 7aafcdf..a678716 100644
--- a/pts-core/options/analyze_image_delta.php
+++ b/pts-core/options/analyze_image_delta.php
@@ -24,7 +24,7 @@ class analyze_image_delta implements pts_option_interface
 {
     public static function required_function_sets()
     {
-        return array("run", "iqc");
+        return array("run");
     }
     public static function argument_checks()
     {
@@ -106,14 +106,14 @@ class analyze_image_delta implements pts_option_interface
             {
                 for($y = 0; $y < $img_height; $y++)
                 {
-                    $base_image_color = pts_rgb_gd_color_at($base_img, $x, $y);
-                    $compare_image_color = pts_rgb_gd_color_at($compare_img, $x, $y);
+                    $base_image_color = pts_image::rgb_gd_color_at($base_img, $x, $y);
+                    $compare_image_color = pts_image::rgb_gd_color_at($compare_img, $x, $y);

-                    if($base_image_color == $compare_image_color || pts_rgb_int_diff($base_image_color, $compare_image_color) < 9)
+                    if($base_image_color == $compare_image_color || pts_image::rgb_int_diff($base_image_color, $compare_image_color) < 9)
                     {
-                        if(($cords = pts_color_pixel_delta($base_img, $compare_img, $x, $y)))
+                        if(($cords = pts_image::color_pixel_delta($base_img, $compare_img, $x, $y)))
                         {
-                            $pixel_rgb = pts_rgb_gd_color_at($delta_img, $cords[0], $cords[1]);
+                            $pixel_rgb = pts_image::rgb_gd_color_at($delta_img, $cords[0], $cords[1]);
                             $color_invert = imagecolorresolve($delta_img, 255 - $pixel_rgb[0], 255 - $pixel_rgb[1], 255 - $pixel_rgb[2]);
                             imagesetpixel($delta_img, $x, $y, $color_invert);
                             $img_changed = true;
diff --git a/pts-core/options/gui_gtk.php b/pts-core/options/gui_gtk.php
index afea233..b554e7d 100644
--- a/pts-core/options/gui_gtk.php
+++ b/pts-core/options/gui_gtk.php
@@ -24,7 +24,7 @@ class gui_gtk implements pts_option_interface
 {
     public static function required_function_sets()
     {
-        return array("gui", "run", "gtk", "install", "install_dependencies", "comparisons", "unit_caching");
+        return array("gui", "run", "gtk", "install", "install_dependencies", "comparisons");
     }
     public static function run($r)
     {
@@ -82,21 +82,21 @@ class gui_gtk implements pts_option_interface
         }

         $startup_tasks = array(
-        array("pts_cache_hardware_calls", "Building Hardware Information"),
-        array("pts_cache_software_calls", "Building Software Information"),
-        array("pts_cache_suite_calls", "Caching Suite Information"),
-        array("pts_cache_test_calls", "Caching Test Information"),
-        array("pts_download_all_generic_reference_system_comparison_results", "Downloading Reference Comparison Results"),
-        array("pts_generic_reference_system_build_cache", "Building Reference Comparison Cache")
+        array("Building Hardware Information", array("pts_client", "cache_hardware_calls")),
+        array("Building Software Information", array("pts_client", "cache_software_calls")),
+        array("Caching Suite Information", array("pts_client", "cache_suite_calls")),
+        array("Caching Test Information", array("pts_client", "cache_test_calls")),
+        array("Downloading Reference Comparison Results", "pts_download_all_generic_reference_system_comparison_results"),
+        array("Building Reference Comparison Cache", "pts_generic_reference_system_build_cache")
         );

         $progress_window = new pts_gtk_simple_progress_window();

         $tasks_completed = 0;
         $task_count = count($startup_tasks);
-        foreach($startup_tasks as $function => $task)
+        foreach($startup_tasks as &$task)
         {
-            list($task_call, $task_string) = $task;
+            list($task_string, $task_call) = $task;
             $progress_window->update_progress_bar(($tasks_completed / $task_count) * 100, $task_string);
             call_user_func($task_call);
             $tasks_completed++;
diff --git a/pts-core/options/run_test.php b/pts-core/options/run_test.php
index b824731..a74bed0 100644
--- a/pts-core/options/run_test.php
+++ b/pts-core/options/run_test.php
@@ -24,13 +24,13 @@ class run_test implements pts_option_interface
 {
     public static function required_function_sets()
     {
-        return array("run", "batch", "execution");
+        return array("run", "execution");
     }
     public static function run($to_run_identifiers)
     {
         if(pts_read_assignment("IS_BATCH_MODE"))
         {
-            if(!pts_batch_mode_configured() && !pts_is_assignment("AUTOMATED_MODE"))
+            if(pts_config::read_bool_config(P_OPTION_BATCH_CONFIGURED, "FALSE") == false && !pts_is_assignment("AUTOMATED_MODE"))
             {
                 echo pts_string_header("The batch mode must first be configured.\nRun: phoronix-test-suite batch-setup");
                 return false;
@@ -91,7 +91,7 @@ class run_test implements pts_option_interface
                     }
                 }

-                if(pts_read_assignment("IS_BATCH_MODE") && pts_batch_run_all_test_options())
+                if(pts_read_assignment("IS_BATCH_MODE") && pts_config::read_bool_config(P_OPTION_BATCH_TESTALLOPTIONS, "TRUE"))
                 {
                     list($test_arguments, $test_arguments_description) = pts_generate_batch_run_options($to_run);
                 }
@@ -266,7 +266,7 @@ class run_test implements pts_option_interface
                 }

                 // Prompt Description
-                if(!pts_is_assignment("AUTOMATED_MODE") && !pts_read_assignment("FINISH_INCOMPLETE_RUN") && !pts_is_assignment("RECOVER_RUN") && (pts_read_assignment("IS_BATCH_MODE") == false || pts_batch_prompt_test_description()))
+                if(!pts_is_assignment("AUTOMATED_MODE") && !pts_read_assignment("FINISH_INCOMPLETE_RUN") && !pts_is_assignment("RECOVER_RUN") && (pts_read_assignment("IS_BATCH_MODE") == false || pts_config::read_bool_config(P_OPTION_BATCH_PROMPTDESCRIPTION, "FALSE")))
                 {
                     if(empty($test_description))
                &nb