diff --git a/CHANGELOG.md b/CHANGELOG.md
index c3b4f25c..75df39d7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 This file documents all notable changes made to ITFlow.
 
 ## [25.10.1]
+- Deprecation Notice: `/scripts/cron_mail_queue.php` , `/scripts/cron_ticket_email_parser.php` , `/scripts/cron.php` `/scripts/cron_domain_refresher.php`, `/scripts/cron_certificate_refresher.php` are being phased out. Please transition to `/cron/mail_queue.php` , `/cron/ticket_email_parser.php`, `/cron/cron.php`, `/cron/domain_refresher.php`, `/cron/certificate_refresher.php` These older scripts will be removed in the November 25.11 release—update accordingly. 25.10.1 installs have the script already configured.
 
 ### Fixes
 - Fix regression missing custom Favicon.
@@ -14,11 +15,14 @@ This file documents all notable changes made to ITFlow.
 - Prevent open redirects upon agent login.
 - Fix regression on switching to Webklex IMAP to allow for no SSL/TLS in IMAP.
 - Fix Setup Redirect not behaving properly when setup hasnt been performed.
+- Added Server Document Root Var to several includes, headers, footers files to allow includes from deeper directory strutures such as the new custom directories.
 
 ### Added / Changed
 - Support for HTML Signatures.
 - Add Edit Project Functionality in a ticket.
-
+- Added more custom locations: /cron/custom/, /scripts/custom/, /api/v1/custom/, /setup/custom/.
+- Copied `/scripts/cron.php` `/scripts/cron_domain_refresher.php`, `/scripts/cron_certificate_refresher.php` to `/cron/cron.php`, `/cron/domain_refresher.php`, `/cron/certificate_refresher.php`. See Above!
+-
 
 ## [25.10]
 
diff --git a/guest/guest_pay_invoice_stripe.php b/guest/guest_pay_invoice_stripe.php
index 21526022..894c133a 100644
--- a/guest/guest_pay_invoice_stripe.php
+++ b/guest/guest_pay_invoice_stripe.php
@@ -1,6 +1,6 @@
 <?php
 
-require_once 'includes/guest_header.php';
+require_once 'includes/inc_all_guest.php';
 
 DEFINE("WORDING_PAYMENT_FAILED", "<br><h2>There was an error verifying your payment. Please contact us for more information before attempting payment again.</h2>");
 
@@ -300,4 +300,4 @@ if (isset($_GET['invoice_id'], $_GET['url_key']) && !isset($_GET['payment_intent
     exit(WORDING_PAYMENT_FAILED);
 }
 
-require_once 'includes/guest_footer.php';
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
diff --git a/guest/guest_view_invoice.php b/guest/guest_view_invoice.php
index 4e1ed287..35f98438 100644
--- a/guest/guest_view_invoice.php
+++ b/guest/guest_view_invoice.php
@@ -1,10 +1,10 @@
 <?php
 
-require_once "includes/guest_header.php";
+require_once "includes/inc_all_guest.php";
 
 if (!isset($_GET['invoice_id'], $_GET['url_key'])) {
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -25,7 +25,7 @@ $sql = mysqli_query(
 if (mysqli_num_rows($sql) !== 1) {
     // Invalid invoice/key
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -478,4 +478,4 @@ if ($outstanding_invoices_count > 0) { ?>
 
 <?php } // End previous unpaid invoices
 
-require_once "includes/guest_footer.php";
+require_once $_SERVER['DOCUMENT_ROOT']  . '/includes/footer.php';
diff --git a/guest/guest_view_item.php b/guest/guest_view_item.php
index 553da300..023d18b2 100644
--- a/guest/guest_view_item.php
+++ b/guest/guest_view_item.php
@@ -4,7 +4,7 @@ header('Cache-Control: no-store, no-cache, must-revalidate');
 header('Cache-Control: post-check=0, pre-check=0', false);
 header('Pragma: no-cache');
 
-require_once "includes/guest_header.php";
+require_once "includes/inc_all_guest.php";
 
 
 //Initialize the HTML Purifier to prevent XSS
@@ -39,7 +39,7 @@ $currency_format = numfmt_create($company_locale, NumberFormatter::CURRENCY);
 <?php
 if (!isset($_GET['id']) || !isset($_GET['key'])) {
     echo "<div class='alert alert-danger'>Incorrect URL.</div>";
-    include "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -53,7 +53,7 @@ $row = mysqli_fetch_array($sql);
 // Check we got a result
 if (mysqli_num_rows($sql) !== 1 || !$row) {
     echo "<div class='alert alert-danger' >No item to view. Check with the person that sent you this link to ensure it is correct and has not expired.</div>";
-    include "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -61,7 +61,7 @@ if (mysqli_num_rows($sql) !== 1 || !$row) {
 // Check item share is active & hasn't been viewed too many times but allow 0 views as that is consider infinite views
 if ($row['item_active'] !== "1" || ($row['item_view_limit'] > 0 && $row['item_views'] >= $row['item_view_limit'])) {
     echo "<div class='alert alert-danger'>Item cannot be viewed at this time. Check with the person that sent you this link to ensure it is correct and has not expired.</div>";
-    include "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -123,7 +123,7 @@ if ($item_type == "Document") {
 
     if (mysqli_num_rows($doc_sql) !== 1 || !$doc_row) {
         echo "<div class='alert alert-danger'>Error retrieving document to view.</div>";
-        require_once "includes/guest_footer.php";
+        require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
         exit();
     }
@@ -150,7 +150,7 @@ if ($item_type == "Document") {
 
     if (mysqli_num_rows($file_sql) !== 1 || !$file_row) {
         echo "<div class='alert alert-danger'>Error retrieving file.</div>";
-        include "includes/guest_footer.php";
+        require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
         exit();
     }
@@ -171,7 +171,7 @@ if ($item_type == "Document") {
     $credential_row = mysqli_fetch_array($credential_sql);
     if (mysqli_num_rows($credential_sql) !== 1 || !$credential_row) {
         echo "<div class='alert alert-danger'>Error retrieving login.</div>";
-        include "includes/guest_footer.php";
+        require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
         exit();
     }
@@ -274,6 +274,4 @@ if ($item_type == "Document") {
 </div>
 
 <?php
-require_once "includes/guest_footer.php";
-
-?>
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
diff --git a/guest/guest_view_quote.php b/guest/guest_view_quote.php
index 7497f654..c791487d 100644
--- a/guest/guest_view_quote.php
+++ b/guest/guest_view_quote.php
@@ -1,11 +1,11 @@
 <?php
 
-require_once "includes/guest_header.php";
+require_once $_SERVER['DOCUMENT_ROOT'] . '/guest/includes/inc_all_guest.php';
 
 
 if (!isset($_GET['quote_id'], $_GET['url_key'])) {
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -27,7 +27,7 @@ $sql = mysqli_query(
 if (mysqli_num_rows($sql) !== 1) {
     // Invalid quote/key
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -133,7 +133,7 @@ if ($quote_status == "Draft" || $quote_status == "Sent" || $quote_status == "Vie
         <div class="row mb-3">
             <?php if (file_exists("../uploads/settings/$company_logo")) { ?>
             <div class="col-sm-2">
-                <img class="img-fluid" src="<?php echo "../uploads/settings/$company_logo"; ?>" alt="Company logo">
+                <img class="img-fluid" src="<?php echo "/uploads/settings/$company_logo"; ?>" alt="Company logo">
             </div>
             <?php } ?>
             <div class="col-sm-6 <?php if (!file_exists("../uploads/settings/$company_logo")) { echo "col-sm-8"; } ?>">
@@ -301,4 +301,4 @@ if ($quote_status == "Draft" || $quote_status == "Sent" || $quote_status == "Vie
 
 <?php
 require_once "guest_quote_upload_file_modal.php";
-require_once "includes/guest_footer.php";
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
diff --git a/guest/guest_view_ticket.php b/guest/guest_view_ticket.php
index bab520f6..ecd45749 100644
--- a/guest/guest_view_ticket.php
+++ b/guest/guest_view_ticket.php
@@ -1,6 +1,6 @@
 <?php
 
-require_once "includes/guest_header.php";
+require_once "includes/inc_all_guest.php";
 
 //Initialize the HTML Purifier to prevent XSS
 require "../plugins/htmlpurifier/HTMLPurifier.standalone.php";
@@ -12,7 +12,7 @@ $purifier = new HTMLPurifier($purifier_config);
 
 if (!isset($_GET['ticket_id'], $_GET['url_key'])) {
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
     exit();
 }
 
@@ -47,7 +47,7 @@ $ticket_sql = mysqli_query($mysqli,
 if (mysqli_num_rows($ticket_sql) !== 1) {
     // Invalid invoice/key
     echo "<br><h2>Oops, something went wrong! Please raise a ticket if you believe this is an error.</h2>";
-    require_once "includes/guest_footer.php";
+    require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
 
     exit();
 }
@@ -210,7 +210,7 @@ if ($ticket_row) {
 
     ?>
 
-    <script src="../js/pretty_content.js"></script>
+    <script src="/js/pretty_content.js"></script>
 
     <?php } else {
         echo "Ticket ID not found!";
@@ -221,4 +221,4 @@ if ($ticket_row) {
 </div>
 
 <?php
-require_once "includes/guest_footer.php";
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/footer.php';
diff --git a/guest/includes/guest_footer.php b/guest/includes/guest_footer.php
deleted file mode 100644
index 01c63d4a..00000000
--- a/guest/includes/guest_footer.php
+++ /dev/null
@@ -1,29 +0,0 @@
-        </div><!-- /.container-fluid -->
-      </div>
-      <!-- /.content -->
-    </div>
-    <!-- /.content-wrapper -->
-  </div>
-  <!-- ./wrapper -->
-
-  <!-- REQUIRED SCRIPTS -->
-  <?php require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/inc_confirm_modal.php'; ?>
-
-  <!-- jQuery -->
-  <script src="/plugins/jquery/jquery.min.js"></script>
-  <!-- Bootstrap 4 -->
-  <script src="/plugins/bootstrap/js/bootstrap.bundle.min.js"></script>
-  <!-- AdminLTE App -->
-  <script src="/plugins/adminlte/js/adminlte.min.js"></script>
-  <!-- Custom js -->
-  <script src="/plugins/tempusdominus-bootstrap-4/js/tempusdominus-bootstrap-4.min.js"></script>
-  <script src="/plugins/moment/moment.min.js"></script>
-  <script src='/plugins/daterangepicker/daterangepicker.js'></script>
-  <script src='/plugins/select2/js/select2.min.js'></script>
-  <script src='/plugins/inputmask/inputmask.min.js'></script>
-  <script src="/js/app.js"></script>
-  <script src="/js/pretty_content.js"></script>
-  <script src="/js/confirm_modal.js"></script>
-
-  </body>
-</html>
diff --git a/guest/includes/guest_header.php b/guest/includes/guest_header.php
index e1d907a3..c45cdac3 100644
--- a/guest/includes/guest_header.php
+++ b/guest/includes/guest_header.php
@@ -1,27 +1,3 @@
-<?php
-
-require_once $_SERVER['DOCUMENT_ROOT'] . '/config.php';
-require_once $_SERVER['DOCUMENT_ROOT'] . '/functions.php';
-require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/load_global_settings.php';
-
-session_start();
-
-// Set Timezone
-require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/inc_set_timezone.php';
-
-$ip = sanitizeInput(getIP());
-$user_agent = sanitizeInput($_SERVER['HTTP_USER_AGENT']);
-$os = sanitizeInput(getOS($user_agent));
-$browser = sanitizeInput(getWebBrowser($user_agent));
-
-// Get Company Name
-$sql = mysqli_query($mysqli, "SELECT company_name FROM companies WHERE company_id = 1");
-$row = mysqli_fetch_array($sql);
-
-$session_company_name = $row['company_name'];
-
-?>
-
 <!DOCTYPE html>
 <html lang="en">
 <head>
@@ -51,32 +27,10 @@ $session_company_name = $row['company_name'];
     <link rel="stylesheet" href="/plugins/select2-bootstrap4-theme/select2-bootstrap4.min.css">
     <link rel="stylesheet" href='/plugins/daterangepicker/daterangepicker.css'>
 
+    <!-- Scripts -->
+    <script src="/plugins/jquery/jquery.min.js"></script>
+    <script src="/plugins/toastr/toastr.min.js"></script>
+
 </head>
 <body class="layout-top-nav">
-<div class="wrapper text-sm">
-
-    <!-- Content Wrapper. Contains page content -->
-    <div class="content-wrapper">
-
-        <!-- Main content -->
-        <div class="content">
-            <div class="container">
-
-                <?php
-                //Alert Feedback
-                if (!empty($_SESSION['alert_message'])) {
-                    if (!isset($_SESSION['alert_type'])) {
-                        $_SESSION['alert_type'] = "info";
-                    }
-                    ?>
-                    <div class="alert alert-<?php echo $_SESSION['alert_type']; ?>" id="alert">
-                        <?php echo nullable_htmlentities($_SESSION['alert_message']); ?>
-                        <button class='close' data-dismiss='alert'>&times;</button>
-                    </div>
-                    <?php
-
-                    unset($_SESSION['alert_type']);
-                    unset($_SESSION['alert_message']);
-
-                }
-                ?>
+    <div class="wrapper text-sm">
\ No newline at end of file
diff --git a/guest/includes/inc_all_guest.php b/guest/includes/inc_all_guest.php
new file mode 100644
index 00000000..b30592a3
--- /dev/null
+++ b/guest/includes/inc_all_guest.php
@@ -0,0 +1,32 @@
+<?php
+// Configuration & core
+require_once $_SERVER['DOCUMENT_ROOT'] . '/config.php';
+require_once $_SERVER['DOCUMENT_ROOT'] . '/functions.php';
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/load_global_settings.php';
+
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/session_init.php';
+
+// Set Timezone
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/inc_set_timezone.php';
+
+$ip = sanitizeInput(getIP());
+$user_agent = sanitizeInput($_SERVER['HTTP_USER_AGENT']);
+$os = sanitizeInput(getOS($user_agent));
+$browser = sanitizeInput(getWebBrowser($user_agent));
+
+// Get Company Name
+$sql = mysqli_query($mysqli, "SELECT company_name FROM companies WHERE company_id = 1");
+$row = mysqli_fetch_array($sql);
+
+$session_company_name = $row['company_name'];
+
+// Page setup
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/page_title.php';
+
+// Layout UI
+require_once $_SERVER['DOCUMENT_ROOT'] . '/guest/includes/guest_header.php';
+
+// Wrapper & alerts
+require_once $_SERVER['DOCUMENT_ROOT'] . '/guest/includes/inc_wrapper.php';
+require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/inc_alert_feedback.php';
+//require_once $_SERVER['DOCUMENT_ROOT'] . '/includes/filter_header.php';
diff --git a/guest/includes/inc_wrapper.php b/guest/includes/inc_wrapper.php
new file mode 100644
index 00000000..76b451d2
--- /dev/null
+++ b/guest/includes/inc_wrapper.php
@@ -0,0 +1,6 @@
+<!-- Content Wrapper. Contains page content -->
+<div class="content-wrapper">
+
+    <!-- Main content -->
+    <div class="content">
+        <div class="container">
\ No newline at end of file