diff --git a/config/deprecatedFiles.lst b/config/deprecatedFiles.lst
new file mode 100644
index 000000000..43cb64059
--- /dev/null
+++ b/config/deprecatedFiles.lst
@@ -0,0 +1,107 @@
+checksum.txt
+features/backend/projects/database_connections/main_tests_database_connections_sqlserver.feature
+features/backend/projects/project_export_import/main_tests_project_export_import.feature
+gulliver/core/Session/PmSessionHandler.php
+gulliver/js/codemirror/addon/hint/pig-hint.js
+gulliver/js/codemirror/addon/hint/python-hint.js
+gulliver/js/codemirror/addon/merge/dep/diff_match_patch.js
+gulliver/js/codemirror/bower.json
+gulliver/js/codemirror/keymap/extra.js
+gulliver/js/codemirror/mode/less
+gulliver/js/codemirror/mode/rpm/changes/changes.js
+gulliver/js/codemirror/mode/rpm/spec
+gulliver/js/codemirror/test/lint/acorn.js
+gulliver/js/codemirror/test/lint/lint.js
+gulliver/js/codemirror/test/lint/walk.js
+gulliver/js/dveditor
+gulliver/js/highlight
+gulliver/js/json/core/json.js
+gulliver/js/md5/core/md5.js
+gulliver/system/class.database_mssql.php
+gulliver/system/class.dvEditor.php
+gulliver/system/class.functionTest.php
+gulliver/system/class.testTools.php
+gulliver/system/class.unitTest.php
+gulliver/system/class.ymlDomain.php
+gulliver/system/class.ymlTestCases.php
+gulliver/thirdparty
+rbac/engine/content
+rbac/engine/db/dbmodule_processmaker.php
+rbac/engine/includes
+rbac/engine/menus
+rbac/engine/methods
+rbac/engine/pre_processor.php
+rbac/engine/tables
+rbac/engine/templates
+rbac/engine/xmlform
+rbac/public_html/skins/JSForms.js
+virtualhost.conf.example
+workflow/engine/classes/class.jrml.php
+workflow/engine/classes/entities/AppSolrQueue.php
+workflow/engine/classes/entities/Base.php
+workflow/engine/classes/entities/FacetGroup.php
+workflow/engine/classes/entities/FacetInterfaceRequest.php
+workflow/engine/classes/entities/FacetInterfaceResult.php
+workflow/engine/classes/entities/FacetItem.php
+workflow/engine/classes/entities/FacetRequest.php
+workflow/engine/classes/entities/FacetResult.php
+workflow/engine/classes/entities/SelectedFacetGroupItem.php
+workflow/engine/classes/entities/SolrQueryResult.php
+workflow/engine/classes/entities/SolrRequestData.php
+workflow/engine/classes/entities/SolrUpdateDocument.php
+workflow/engine/classes/triggers/api/class.zimbraApi.php
+workflow/engine/controllers/dashboard.php
+workflow/engine/controllers/installer.php
+workflow/engine/includes/inc.JSForms.php
+workflow/engine/js/cases/core/cases_Step_Pmdynaform.js
+workflow/engine/methods/cases/casesDemo.php
+workflow/engine/methods/cases/cases_Scheduler_Save.php
+workflow/engine/methods/cases/cases_Scheduler_Update.php
+workflow/engine/methods/cases/proxyPMTablesSaveFields.php
+workflow/engine/methods/cases/saveFormSupervisor.php
+workflow/engine/methods/controls/buscador.php
+workflow/engine/methods/dbConnections/genericDbConnections.php
+workflow/engine/methods/login/dbInfo.php
+workflow/engine/methods/services/processHeartBeat_Ajax.php
+workflow/engine/methods/services/soap.php
+workflow/engine/methods/services/wsdl.php
+workflow/engine/methods/services/wso2.php
+workflow/engine/methods/setup/jasper.php
+workflow/engine/methods/setup/webServices.php
+workflow/engine/methods/setup/webServicesAjax.php
+workflow/engine/methods/setup/webServicesList.php
+workflow/engine/plugins/openFlash.php
+workflow/engine/plugins/openFlash/chart-data.php
+workflow/engine/plugins/openFlash/chart.php
+workflow/engine/plugins/openFlash/class.openFlash.php
+workflow/engine/plugins/openFlash/open-flash-chart.php
+workflow/engine/plugins/openFlash/open_flash_chart_object.php
+workflow/engine/plugins/openFlash/public_html/open-flash-chart.swf
+workflow/engine/plugins/openFlash/public_html/swfobject.js
+workflow/engine/plugins/openFlash/setupPage.xml
+workflow/engine/plugins/pmosCommunity.php
+workflow/engine/plugins/pmosCommunity/chart-data.php
+workflow/engine/plugins/pmosCommunity/chart.php
+workflow/engine/plugins/pmosCommunity/class.pmosCommunity.php
+workflow/engine/plugins/pmosCommunity/config/databases.php
+workflow/engine/plugins/pmosCommunity/config/setup.conf
+workflow/engine/plugins/pmosCommunity/drawChart.php
+workflow/engine/plugins/pmosCommunity/open-flash-chart.php
+workflow/engine/plugins/pmosCommunity/open_flash_chart_object.php
+workflow/engine/plugins/pmosCommunity/public_html/open-flash-chart.swf
+workflow/engine/plugins/pmosCommunity/public_html/swfobject.js
+workflow/engine/plugins/pmosCommunity/setupPage.xml
+workflow/engine/skinEngine/base/images/updating/page_background.png
+workflow/engine/skinEngine/neoclassic/images/updating/page_background.png
+workflow/engine/src/ProcessMaker/Services/Api/Test2.php
+workflow/engine/src/ProcessMaker/Services/Api/Test3.php
+workflow/engine/src/Tests
+workflow/engine/templates/cases/casesDemo.html
+workflow/engine/templates/cases/cases_Step_Pmdynaform.html
+workflow/engine/templates/cases/cases_Step_Pmdynaform_Preview.html
+workflow/engine/templates/cases/cases_Step_Pmdynaform_View.html
+workflow/engine/templates/login/init.js
+workflow/engine/templates/reportTables/mainLoad.php
+workflow/engine/test
+workflow/public_html/skins/JSForms.js
+workflow/public_html/skins/ajax.js
diff --git a/workflow/engine/classes/WorkspaceTools.php b/workflow/engine/classes/WorkspaceTools.php
index 21d403cd5..3e4d4dfca 100644
--- a/workflow/engine/classes/WorkspaceTools.php
+++ b/workflow/engine/classes/WorkspaceTools.php
@@ -233,6 +233,12 @@ class WorkspaceTools
             $arrayOptTranslation = ['updateXml' => true, 'updateMafe' => true];
         }
 
+        $start = microtime(true);
+        CLI::logging("> Remove deprecated files...\n");
+        $this->removeDeprecatedFiles();
+        $stop = microtime(true);
+        CLI::logging("<*>   Remove deprecated files took " . ($stop - $start) . " seconds.\n");
+
         $start = microtime(true);
         CLI::logging("> Updating database...\n");
         $this->upgradeDatabase($onedb);
@@ -2000,6 +2006,12 @@ class WorkspaceTools
                 }
             }
 
+            $start = microtime(true);
+            CLI::logging("> Remove deprecated files...\n");
+            $workspace->removeDeprecatedFiles();
+            $stop = microtime(true);
+            CLI::logging("<*>   Remove deprecated files took " . ($stop - $start) . " seconds.\n");
+
             if (($pmVersionWorkspaceToRestore != '') && (version_compare(
                         $pmVersionWorkspaceToRestore . "",
                         $pmVersion . "",
@@ -4560,4 +4572,28 @@ class WorkspaceTools
                 . "WHERE ASSIGNEE_ID = 0");
         $con->commit();
     }
+    
+    /**
+     * Remove deprecated files and directory.
+     */
+    public function removeDeprecatedFiles()
+    {
+        $deprecatedFiles = PATH_TRUNK . PATH_SEP . 'config' . PATH_SEP . 'deprecatedFiles.lst';
+        if (file_exists($deprecatedFiles)) {
+            $handle = fopen($deprecatedFiles, 'r');
+            if ($handle) {
+                while (($line = fgets($handle)) !== false) {
+                    $line = trim($line, "\n");
+                    CLI::logging("> Remove file/folder " . $line . " ");
+                    if (file_exists($line)) {
+                        G::rm_dir($line);
+                        CLI::logging("[OK]\n");
+                    } else {
+                        CLI::logging("[Already removed]\n");
+                    }
+                }
+                fclose($handle);
+            }
+        }
+    }
 }