diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index e408b48..72f4d92 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -25,12 +25,14 @@ When generating code for this repository:
 
 ```
 maint/                # Repository root (install to plugins/maint/ in Cacti)
-├── locales/             # Internationalization files
-├── functions.php          # Runtime maintenance checks (plugin_maint_check_* -> plugin_maint_check_schedule)
-├── maint.php                # Main UI/controller: CRUD schedules, tabbed views, host associations
-├── INFO                        # Plugin metadata (name, version, compat)
+├── includes/         # Library/helper files, require_once'd from the entry points
+│   ├── database.php  # Schema management: table defs + create/upgrade helpers
+│   └── functions.php # Runtime maintenance checks (plugin_maint_check_* -> plugin_maint_check_schedule)
+├── locales/          # Internationalization files
+├── maint.php         # Main UI/controller: CRUD schedules, tabbed views, host associations
+├── INFO              # Plugin metadata (name, version, compat)
 ├── README.md
-└── setup.php                     # Plugin entry points and hooks (menu, realms, device actions, maintenance hook)
+└── setup.php         # Plugin entry points and hooks (menu, realms, device actions, maintenance hook)
 ```
 
 ## Naming Conventions
@@ -77,7 +79,14 @@ arithmetic, strict `===` comparisons).
 
 ## Database Operations
 
-Tables are created in `maint_setup_database()` via `api_plugin_db_table_create()`; `plugin_maint_check_schedule()` updates `stime`/`etime` for recurring schedules when windows pass, and schedule listing in `maint.php` uses it to compute "Active" state.
+All schema management lives in `includes/database.php` (the thold model), not in `setup.php`. `setup.php`'s
+install/upgrade paths `require_once($config['base_path'] . '/plugins/maint/includes/database.php')` and
+delegate. Each table is defined once (`maint_schedules_table_data()`, `maint_hosts_table_data()`) and created
+via `api_plugin_db_table_create('maint', ...)`; `plugin_maint_check_upgrade()` version-gates against
+`plugin_config`, refreshes the schema through `maint_upgrade_tables()` (`db_update_table()` when the table
+exists, create fallback when missing), and updates the full `plugin_config` row on a version change.
+`plugin_maint_check_schedule()` (in `includes/functions.php`) updates `stime`/`etime` for recurring schedules
+when windows pass, and schedule listing in `maint.php` uses it to compute "Active" state.
 
 ## Internationalization
 
@@ -126,7 +135,7 @@ Document all changes via commit history; use descriptive commit messages referen
 
 - Translatable strings are managed with GNU gettext via `locales/build_gettext.sh`. `locales/po/cacti.pot` is the source template; Weblate owns syncing the per-language `.po`/`.mo` files from it.
 - **Never commit the per-language `.po` or compiled `.mo` files** (`locales/po/*.po`, `locales/LC_MESSAGES/*.mo`) in a plugin PR. Weblate is the sole owner of those catalogs, and regenerating them here produces spurious diffs and merge conflicts. `locales/po/cacti.pot` is the ONLY translation artifact a PR may add or modify.
-- When a pull request adds or changes a string wrapped in `__()`/`__n()`/`__esc()`/`__x()`/`__xn()`/`__gettext()`, run `locales/build_gettext.sh` before pushing and stage `locales/po/cacti.pot` only. `build_gettext.sh` also rewrites the `.po`/`.mo` files as a side effect; revert those before committing (`git checkout -- locales/po/*.po locales/LC_MESSAGES`), or run only the `xgettext` step that targets `cacti.pot`.
+- When a pull request adds or changes a string wrapped in `__()`/`__n()`/`__esc()`/`__x()`/`__xn()`/`__gettext()`, run `locales/build_gettext.sh` before pushing and stage `locales/po/cacti.pot` only. `build_gettext.sh` also rewrites the `.po`/`.mo` files as a side effect; revert those before committing (`git checkout -- locales/po/*.po locales/LC_MESSAGES`), or run only the `xgettext` step that targets `cacti.pot`.
 
 ## References
 
@@ -150,6 +159,11 @@ existing code or adding new code, not just in dedicated cleanup passes:
 - **i18n text domain.** Every `__()`/`__esc()` call must include this plugin's text domain as the
   final argument, except when deliberately comparing against a literal, untranslated Cacti-core
   label.
+- **File inclusion uses `require`/`require_once`.** Always use `require`/`require_once` (never
+  `include`/`include_once`) so a missing dependency fails fast and loudly. Keep library/helper files
+  (e.g. `functions.php`, `includes/database.php`) under `includes/` and reference them from that path;
+  entry points (`maint.php`, `setup.php`) stay in the plugin root. A hook registered for a function that
+  lives in `includes/functions.php` must pass `'includes/functions.php'` as its file argument.
 - **Plugin table-creation API.** Use `api_plugin_db_table_create()`/`api_plugin_db_add_column()`
   (from Cacti core's `lib/plugins.php`) instead of raw `CREATE TABLE`/`ALTER TABLE ... ADD COLUMN`.
   Both are idempotent (safe no-ops when already applied), so the same call can run unconditionally
@@ -158,3 +172,7 @@ existing code or adding new code, not just in dedicated cleanup passes:
   line, `@param` lines, a blank comment line, then `@return`. Infer parameter/return types from
   actual usage; don't change the function's real type-hints in the same pass (let static analysis
   flag mismatches separately). Skip vendored third-party library files.
+
+## File manifest & upgrade pruning
+
+The plugin ships a root `manifest.json` with three arrays: `tombstones` (files/directories older versions shipped that have since moved or been removed), `expected` (the top-level files and directories that ship today, directories written with a trailing `/`), and `whitelist` (paths holding user data that must never be touched). Keep `expected` current: CI runs `tests/bin/validate-manifest.php`, which fails on any drift between `expected` and the real top-level tree (it ignores `tests/`, `phpunit.xml`, `.git*`, `.md*`, and whitelisted paths). Custom customer CSS/theme files belong in `expected`, and stylesheets live in `css/` (not `themes/`). On upgrade, `maint_prune_files()` deletes the tombstoned paths, the dev-only `tests/` tree, and the `phpunit.xml` test config, leaves `whitelist`, `.git*`, and `.md*` alone, and logs (without removing) any top-level entry the manifest does not account for. As a safety measure it refuses any tombstone that resolves outside the plugin directory (a tampered manifest.json) and logs a warning for any file or directory it cannot remove. When you move or delete a shipped file, add its old path to `tombstones` and update `expected` in the same change.
diff --git a/.github/workflows/plugin-ci-workflow.yml b/.github/workflows/plugin-ci-workflow.yml
index 2c09779..d3f0560 100644
--- a/.github/workflows/plugin-ci-workflow.yml
+++ b/.github/workflows/plugin-ci-workflow.yml
@@ -89,6 +89,9 @@ jobs:
     - name: Check PHP version
       run: php -v
 
+    - name: Validate plugin manifest (expected-file drift)
+      run: php cacti/plugins/maint/tests/bin/validate-manifest.php
+
     - name: Run apt-get update
       run: sudo apt-get update
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a4d1c76..0ba67bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 --- develop ---
 
+* refactor: Move schema management into includes/database.php (the thold model) and relocate functions.php into includes/; setup.php delegates via require_once, and plugin_maint_check_upgrade() now refreshes the schema via db_update_table(), re-registers the is_device_in_maintenance hook against includes/functions.php, and updates the full plugin_config row on a version change. Switches every file inclusion from include/include_once to require/require_once
 * dev: Enforce patch coverage of changed lines in CI and remove the inert COMPOSER_ROOT_VERSION env from the Pest step
 * feature: Add a standard Cacti search filter to the Maintenance Schedules list that also matches the hostname/description/location/site name of associated Thold devices and the hostname/description of associated Servcheck tests
 * security: Add a version-safe CSP nonce (`plugin_maint_csp_nonce()`) to every inline `<script>` tag so pages stay compatible with Cacti's Content-Security-Policy nonce enforcement, while falling back cleanly on older Cacti releases that lack the `CactiSecureHeaders` class
diff --git a/INFO b/INFO
index 74b97da..e32353c 100644
--- a/INFO
+++ b/INFO
@@ -26,5 +26,5 @@ longname = Maintenance Scheduler
 author = The Cacti Group
 email = 
 homepage = http://cacti.net
-compat = 1.2.0
+compat = 1.2.29
 capabilities = online_view:1, online_mgmt:1, offline_view:0, offline_mgmt:0, remote_collect:0
diff --git a/includes/database.php b/includes/database.php
new file mode 100644
index 0000000..cc08ba6
--- /dev/null
+++ b/includes/database.php
@@ -0,0 +1,137 @@
+<?php
+/*
+ +-------------------------------------------------------------------------+
+ | Copyright (C) 2004-2026 The Cacti Group                                 |
+ |                                                                         |
+ | 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 2          |
+ | 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.                            |
+ +-------------------------------------------------------------------------+
+ | Cacti: The Complete RRDtool-based Graphing Solution                     |
+ +-------------------------------------------------------------------------+
+ | This code is designed, written, and maintained by the Cacti Group. See  |
+ | about.php and/or the AUTHORS file for specific developer information.   |
+ +-------------------------------------------------------------------------+
+ | http://www.cacti.net/                                                   |
+ +-------------------------------------------------------------------------+
+*/
+
+/**
+ * The plugin_maint_schedules table definition (one row per maintenance
+ * schedule), shared by the create path (api_plugin_db_table_create()) and
+ * the upgrade path (db_update_table()) so both stay in sync from a single
+ * definition.
+ *
+ * @return array<string, mixed> The table definition array.
+ */
+function maint_schedules_table_data(): array {
+	$data              = [];
+	$data['columns'][] = ['name' => 'id', 'type' => 'int(11)', 'NULL' => false, 'auto_increment' => true];
+	$data['columns'][] = ['name' => 'enabled', 'type' => 'varchar(3)', 'NULL' => false, 'default' => 'on'];
+	$data['columns'][] = ['name' => 'name', 'type' => 'varchar(128)', 'NULL' => true];
+	$data['columns'][] = ['name' => 'mtype', 'type' => 'int(11)', 'NULL' => false];
+	$data['columns'][] = ['name' => 'stime', 'type' => 'int(22)', 'NULL' => false];
+	$data['columns'][] = ['name' => 'etime', 'type' => 'int(22)', 'NULL' => false];
+	$data['columns'][] = ['name' => 'minterval', 'type' => 'int(11)', 'NULL' => false];
+	$data['primary']   = ['id'];
+	$data['keys'][]    = ['name' => 'mtype', 'columns' => ['mtype']];
+	$data['keys'][]    = ['name' => 'enabled', 'columns' => ['enabled']];
+	$data['type']      = 'InnoDB';
+	$data['comment']   = 'Maintenance Schedules';
+
+	return $data;
+}
+
+/**
+ * The plugin_maint_hosts table definition (maps devices/tests to a
+ * maintenance schedule), shared by the create path
+ * (api_plugin_db_table_create()) and the upgrade path (db_update_table()).
+ *
+ * @return array<string, mixed> The table definition array.
+ */
+function maint_hosts_table_data(): array {
+	$data              = [];
+	$data['columns'][] = ['name' => 'type', 'type' => 'int(6)', 'NULL' => false];
+	$data['columns'][] = ['name' => 'host', 'type' => 'int(12)', 'NULL' => false];
+	$data['columns'][] = ['name' => 'schedule', 'type' => 'int(12)', 'NULL' => false];
+	$data['primary']   = ['type', 'schedule', 'host'];
+	$data['keys'][]    = ['name' => 'type', 'columns' => ['type']];
+	$data['keys'][]    = ['name' => 'schedule', 'columns' => ['schedule']];
+	$data['type']      = 'InnoDB';
+	$data['comment']   = 'Maintenance Schedules Hosts';
+
+	return $data;
+}
+
+/**
+ * Creates this plugin's database tables (plugin_maint_schedules and
+ * plugin_maint_hosts) through Cacti's tracked plugin table API. Called
+ * from plugin_maint_install() during installation, and re-run (safely, as
+ * a no-op for already-applied changes) from maint_upgrade_tables() during
+ * upgrades.
+ *
+ * @return void
+ */
+function maint_setup_database(): void {
+	api_plugin_db_table_create('maint', 'plugin_maint_schedules', maint_create_definition(maint_schedules_table_data()));
+	api_plugin_db_table_create('maint', 'plugin_maint_hosts', maint_create_definition(maint_hosts_table_data()));
+}
+
+/**
+ * Returns a copy of a table definition with its array primary key
+ * normalized to the legacy backtick-joined scalar form. Older Cacti
+ * releases (1.2.0) concatenate data['primary'] straight into the CREATE in
+ * api_plugin_db_table_create(), so an array would render PRIMARY KEY
+ * (`Array`) and break a fresh install; the array form is retained in the
+ * *_table_data() helpers for db_update_table(), which requires it.
+ *
+ * @param array<string, mixed> $data The table definition (array primary).
+ *
+ * @return array<string, mixed> The definition with a scalar primary key.
+ */
+function maint_create_definition(array $data): array {
+	if (isset($data['primary']) && is_array($data['primary'])) {
+		$data['primary'] = implode('`,`', $data['primary']);
+	}
+
+	return $data;
+}
+
+/**
+ * Refreshes this plugin's tables to their current definition on upgrade:
+ * db_update_table() diffs the live schema against each definition and
+ * issues the exact ALTER when the table already exists, otherwise the
+ * table is created outright. Called from plugin_maint_check_upgrade() when
+ * the stored version changes.
+ *
+ * @return bool True when every table reconciled; false when any
+ *              db_update_table()/api_plugin_db_table_create() reported an
+ *              explicit failure, so the caller can skip the version bump
+ *              and retry on the next request.
+ */
+function maint_upgrade_tables(): bool {
+	$success = true;
+
+	foreach ([
+		'plugin_maint_schedules' => maint_schedules_table_data(),
+		'plugin_maint_hosts'     => maint_hosts_table_data(),
+	] as $table => $data) {
+		if (db_table_exists($table)) {
+			$result = db_update_table($table, $data);
+		} else {
+			$result = api_plugin_db_table_create('maint', $table, maint_create_definition($data));
+		}
+
+		if ($result === false) {
+			$success = false;
+		}
+	}
+
+	return $success;
+}
diff --git a/functions.php b/includes/functions.php
similarity index 100%
rename from functions.php
rename to includes/functions.php
diff --git a/maint.php b/maint.php
index c49edf6..2eee730 100644
--- a/maint.php
+++ b/maint.php
@@ -28,8 +28,8 @@
 global $config;
 
 chdir('../../');
-include_once('./include/auth.php');
-include_once($config['base_path'] . '/plugins/maint/functions.php');
+require_once('./include/auth.php');
+require_once($config['base_path'] . '/plugins/maint/includes/functions.php');
 
 define('MAINT_HOST_FILTER_LOC_ANY', '__any'); // internal value unlikely in data
 define('MAINT_HOST_FILTER_LOC_NONE', '__none');
diff --git a/manifest.json b/manifest.json
new file mode 100644
index 0000000..8fead93
--- /dev/null
+++ b/manifest.json
@@ -0,0 +1,17 @@
+{
+    "tombstones": [],
+    "expected": [
+        ".pre-commit-config.yml",
+        "CHANGELOG.md",
+        "INFO",
+        "LICENSE",
+        "README.md",
+        "includes/",
+        "index.php",
+        "locales/",
+        "maint.php",
+        "manifest.json",
+        "setup.php"
+    ],
+    "whitelist": []
+}
diff --git a/phpunit.xml b/phpunit.xml
index 9c70ec8..f790fa4 100644
--- a/phpunit.xml
+++ b/phpunit.xml
@@ -27,8 +27,7 @@
     -->
     <source>
         <include>
-            <file>functions.php</file>
-            <file>maint.php</file>
+            <file>includes/functions.php</file>
             <file>setup.php</file>
         </include>
     </source>
diff --git a/setup.php b/setup.php
index a0bdb32..7a68035 100644
--- a/setup.php
+++ b/setup.php
@@ -75,15 +75,19 @@ function plugin_maint_version(): array {
  * @return void
  */
 function plugin_maint_install(): void {
+	global $config;
+
 	api_plugin_register_hook('maint', 'config_arrays', 'maint_config_arrays', 'setup.php');
 	api_plugin_register_hook('maint', 'draw_navigation_text', 'maint_draw_navigation_text', 'setup.php');
 	api_plugin_register_hook('maint', 'device_edit_top_links', 'maint_device_edit_top_links', 'setup.php');
-	api_plugin_register_hook('maint', 'is_device_in_maintenance', 'plugin_maint_check_cacti_host', 'functions.php');
+	api_plugin_register_hook('maint', 'is_device_in_maintenance', 'plugin_maint_check_cacti_host', 'includes/functions.php');
 	api_plugin_register_hook('maint', 'device_action_array', 'maint_device_action_array', 'setup.php');
 	api_plugin_register_hook('maint', 'device_action_prepare', 'maint_device_action_prepare', 'setup.php');
 	api_plugin_register_hook('maint', 'device_action_execute', 'maint_device_action_execute', 'setup.php');
 	api_plugin_register_realm('maint', 'maint.php', 'Maintenance Schedules', 1);
 
+	require_once($config['base_path'] . '/plugins/maint/includes/database.php');
+
 	maint_setup_database();
 }
 
@@ -101,30 +105,95 @@ function plugin_maint_uninstall(): void {
 }
 
 /**
- * Check plugin configuration
- *
- * Currently a no-op placeholder. Invoked by Cacti's plugin architecture
- * on relevant page loads.
+ * Runs any pending schema/version upgrade for this plugin. Invoked by
+ * Cacti's plugin architecture on relevant page loads.
  *
  * @return bool Always returns true
  */
 function plugin_maint_check_config(): bool {
+	plugin_maint_check_upgrade();
+
 	return true;
 }
 
 /**
  * Upgrade the maintenance plugin
  *
- * Currently a no-op placeholder (this plugin's schema has not required
- * migrations since its initial release). Invoked by Cacti's plugin
- * architecture when an installed plugin's version increases.
+ * Runs any pending schema/version upgrade for this plugin. Invoked by
+ * Cacti's plugin architecture when an installed plugin's version
+ * increases.
  *
- * @return bool Always returns false (no upgrade needed)
+ * @return bool Always returns false
  */
 function plugin_maint_upgrade(): bool {
+	plugin_maint_check_upgrade();
+
 	return false;
 }
 
+/**
+ * Applies any pending schema migration for this plugin on a version change,
+ * based on comparing the installed version recorded in plugin_config
+ * against the current INFO file version. Only runs on plugins.php or
+ * maint.php to avoid the version lookup on every page. Refreshes the schema
+ * through includes/database.php and updates the full plugin_config row.
+ * Called from plugin_maint_check_config()/plugin_maint_upgrade().
+ *
+ * @return void
+ *
+ * @global array  $config           Cacti global configuration array; used
+ *                                   to locate the database/functions
+ *                                   libraries and this plugin's schema file.
+ * @global object $database_default  Reserved/declared for parity with the
+ *                                   included library files; not used
+ *                                   directly here.
+ */
+function plugin_maint_check_upgrade(): void {
+	global $config, $database_default;
+
+	// Only run this check on a page that actually needs the plugin's data.
+	$files = ['plugins.php', 'maint.php'];
+
+	if (isset($_SERVER['PHP_SELF']) && !in_array(basename($_SERVER['PHP_SELF']), $files, true)) {
+		return;
+	}
+
+	require_once($config['library_path'] . '/database.php');
+	require_once($config['library_path'] . '/functions.php');
+	require_once($config['base_path'] . '/plugins/maint/includes/database.php');
+
+	$info = plugin_maint_version();
+
+	if (empty($info['version']) || empty($info['longname']) || empty($info['author']) || empty($info['homepage'])) {
+		return;
+	}
+
+	$current = $info['version'];
+	$old     = db_fetch_cell_prepared('SELECT version FROM plugin_config WHERE directory = ?', ['maint']);
+
+	if ($current != $old) {
+		// Refresh the schema from the shared definition (create when missing,
+		// db_update_table() diff when it already exists). Only record the new
+		// version once every table reconciled, so a failed refresh is retried on
+		// the next request instead of being masked by a now-matching version.
+		if (maint_upgrade_tables()) {
+			// Re-register the is_device_in_maintenance hook so existing installs
+			// pick up the relocated includes/functions.php file. plugin_maint_install()
+			// registers the new path, but it never re-runs on upgrade, and core's
+			// upgrade path only touches plugin_config, never plugin_hooks.
+			api_plugin_register_hook('maint', 'is_device_in_maintenance', 'plugin_maint_check_cacti_host', 'includes/functions.php');
+
+			db_execute_prepared('UPDATE plugin_config
+				SET version = ?, name = ?, author = ?, webpage = ?
+				WHERE directory = ?',
+				[$info['version'], $info['longname'], $info['author'], $info['homepage'], 'maint']);
+
+			// Remove files tombstoned in manifest.json plus the dev-only tests/ tree.
+			maint_prune_files();
+		}
+	}
+}
+
 /**
  * Configure plugin menu arrays and augment roles
  *
@@ -496,39 +565,176 @@ function maint_device_action_execute(string $action): bool {
 /**
  * Setup database tables for maintenance plugin
  *
- * Creates two tables:
- * - plugin_maint_schedules: Stores maintenance schedules
- * - plugin_maint_hosts: Associates hosts with schedules
- * Called from plugin_maint_install() during plugin installation.
+ * Moved to includes/database.php; see maint_setup_database() and
+ * maint_upgrade_tables() there.
+ */
+
+/**
+ * Removes files and directories that a previous version of this plugin
+ * shipped but that have since moved or been deleted, using the tombstone
+ * and whitelist lists in manifest.json. Whitelisted (user-data) paths and
+ * any VCS metadata (.git*) are never touched; the dev-only tests/ tree is
+ * removed. Any path that resolves outside the plugin directory (a tampered
+ * manifest.json) is refused, and any file/directory that cannot be removed
+ * (e.g. read-only) is reported to the Cacti log. Any top-level entry that is
+ * neither expected nor a tombstone nor whitelisted is logged to the Cacti
+ * log and left in place. Called on a plugin version change.
  *
  * @return void
+ *
+ * @global array $config Cacti global configuration array; used to resolve
+ *                       the plugin directory.
  */
-function maint_setup_database(): void {
-	$data              = [];
-	$data['columns'][] = ['name' => 'id', 'type' => 'int(11)', 'NULL' => false, 'auto_increment' => true];
-	$data['columns'][] = ['name' => 'enabled', 'type' => 'varchar(3)', 'NULL' => false, 'default' => 'on'];
-	$data['columns'][] = ['name' => 'name', 'type' => 'varchar(128)', 'NULL' => true];
-	$data['columns'][] = ['name' => 'mtype', 'type' => 'int(11)', 'NULL' => false];
-	$data['columns'][] = ['name' => 'stime', 'type' => 'int(22)', 'NULL' => false];
-	$data['columns'][] = ['name' => 'etime', 'type' => 'int(22)', 'NULL' => false];
-	$data['columns'][] = ['name' => 'minterval', 'type' => 'int(11)', 'NULL' => false];
-	$data['primary']   = 'id';
-	$data['keys'][]    = ['name' => 'mtype', 'columns' => 'mtype'];
-	$data['keys'][]    = ['name' => 'enabled', 'columns' => 'enabled'];
-	$data['type']      = 'InnoDB';
-	$data['comment']   = 'Maintenance Schedules';
-
-	api_plugin_db_table_create('maint', 'plugin_maint_schedules', $data);
-
-	$data              = [];
-	$data['columns'][] = ['name' => 'type', 'type' => 'int(6)', 'NULL' => false];
-	$data['columns'][] = ['name' => 'host', 'type' => 'int(12)', 'NULL' => false];
-	$data['columns'][] = ['name' => 'schedule', 'type' => 'int(12)', 'NULL' => false];
-	$data['primary']   = 'type`,`schedule`,`host';
-	$data['keys'][]    = ['name' => 'type', 'columns' => 'type'];
-	$data['keys'][]    = ['name' => 'schedule', 'columns' => 'schedule'];
-	$data['type']      = 'InnoDB';
-	$data['comment']   = 'Maintenance Schedules Hosts';
-
-	api_plugin_db_table_create('maint', 'plugin_maint_hosts', $data);
+function maint_prune_files(): void {
+	global $config;
+
+	$plugin_dir    = $config['base_path'] . '/plugins/maint';
+	$manifest_path = $plugin_dir . '/manifest.json';
+
+	if (!is_readable($manifest_path)) {
+		return;
+	}
+
+	$manifest = json_decode((string) file_get_contents($manifest_path), true);
+
+	if (!is_array($manifest)) {
+		cacti_log('WARNING: maint manifest.json could not be parsed; skipping file prune', false, 'MAINT');
+
+		return;
+	}
+
+	$tombstones = isset($manifest['tombstones']) && is_array($manifest['tombstones']) ? $manifest['tombstones'] : [];
+	$expected   = isset($manifest['expected'])   && is_array($manifest['expected'])   ? $manifest['expected']   : [];
+	$whitelist  = isset($manifest['whitelist'])  && is_array($manifest['whitelist'])  ? $manifest['whitelist']  : [];
+
+	$protected = function (string $rel) use ($whitelist): bool {
+		if (strncmp($rel, '.git', 4) === 0 || strncmp($rel, '.md', 3) === 0) {
+			return true;
+		}
+
+		foreach ($whitelist as $entry) {
+			$entry = trim((string) $entry, '/');
+
+			if ($entry !== '' && ($rel === $entry
+				|| strncmp($rel, $entry . '/', strlen($entry) + 1) === 0
+				|| strncmp($entry, $rel . '/', strlen($rel) + 1) === 0)) {
+				return true;
+			}
+		}
+
+		return false;
+	};
+
+	// Security: resolve the plugin directory so a tampered manifest.json
+	// cannot steer the prune outside of it.
+	$plugin_real = realpath($plugin_dir);
+
+	// Remove tombstoned (moved/deleted) paths plus the dev-only tests/
+	// tree and the phpunit.xml test configuration.
+	$remove   = $tombstones;
+	$remove[] = 'tests/';
+	$remove[] = 'phpunit.xml';
+
+	foreach ($remove as $rel) {
+		$rel = trim((string) $rel, '/');
+
+		if ($rel === '' || $protected($rel)) {
+			continue;
+		}
+
+		// A tombstone must never contain '.'/'..' segments; a tampered manifest
+		// could use them to escape the plugin directory or target its root.
+		$segments = explode('/', $rel);
+
+		if (in_array('.', $segments, true) || in_array('..', $segments, true)) {
+			cacti_log(sprintf('WARNING: maint prune refused to remove %s: path contains a traversal segment (tampered manifest.json?)', $rel), false, 'MAINT');
+
+			continue;
+		}
+
+		$path = $plugin_dir . '/' . $rel;
+
+		if (!is_link($path) && !file_exists($path)) {
+			continue;
+		}
+
+		// Refuse any path that, after resolving symlinks and ../ segments,
+		// escapes the plugin directory (protects user data from a tampered
+		// manifest.json).
+		$anchor = is_link($path) ? dirname($path) : $path;
+		$real   = realpath($anchor);
+
+		if ($real === false || ($real !== $plugin_real && strncmp($real, $plugin_real . DIRECTORY_SEPARATOR, strlen((string) $plugin_real) + 1) !== 0)) {
+			cacti_log(sprintf('WARNING: maint prune refused to remove %s: path resolves outside the plugin directory (tampered manifest.json?)', $rel), false, 'MAINT');
+
+			continue;
+		}
+
+		if (is_dir($path) && !is_link($path)) {
+			$removed = maint_rmtree($path);
+		} else {
+			$removed = @unlink($path);
+		}
+
+		if (!$removed) {
+			cacti_log(sprintf('WARNING: maint upgrade could not remove %s (check file/directory permissions)', $rel), false, 'MAINT');
+		}
+	}
+
+	// Surface any top-level entry the manifest does not account for.
+	$known = [];
+
+	foreach (array_merge($expected, $tombstones) as $entry) {
+		$top = explode('/', trim((string) $entry, '/'))[0];
+
+		if ($top !== '') {
+			$known[$top] = true;
+		}
+	}
+
+	$entries = scandir($plugin_dir);
+
+	foreach (($entries !== false ? $entries : []) as $entry) {
+		if ($entry === '.' || $entry === '..' || $entry === 'tests' || $entry === 'phpunit.xml' || $protected($entry) || isset($known[$entry])) {
+			continue;
+		}
+
+		cacti_log(sprintf('WARNING: maint upgrade found a file/directory not described in manifest.json: %s (left in place)', $entry), false, 'MAINT');
+	}
+}
+
+/**
+ * Recursively deletes a directory and its contents. Symlinks are removed
+ * without being followed. Helper for maint_prune_files().
+ *
+ * @param string $dir Absolute path to the directory to remove.
+ *
+ * @return bool True if the directory and everything under it was removed;
+ *              false if any entry could not be deleted.
+ */
+function maint_rmtree(string $dir): bool {
+	$entries = scandir($dir);
+	$ok      = true;
+
+	foreach (($entries !== false ? $entries : []) as $entry) {
+		if ($entry === '.' || $entry === '..') {
+			continue;
+		}
+
+		$path = $dir . '/' . $entry;
+
+		if (is_dir($path) && !is_link($path)) {
+			if (!maint_rmtree($path)) {
+				$ok = false;
+			}
+		} elseif (!@unlink($path)) {
+			$ok = false;
+		}
+	}
+
+	if (!@rmdir($dir)) {
+		$ok = false;
+	}
+
+	return $ok;
 }
diff --git a/tests/Security/AuthGuardTest.php b/tests/Security/AuthGuardTest.php
index c669ddf..05008fe 100644
--- a/tests/Security/AuthGuardTest.php
+++ b/tests/Security/AuthGuardTest.php
@@ -39,7 +39,7 @@
 
 	it('validates numeric IDs from request variables before DB queries', function () {
 		$uiFiles = array(
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		);
 
diff --git a/tests/Security/OutputEscapingTest.php b/tests/Security/OutputEscapingTest.php
index 1fede6b..92b552e 100644
--- a/tests/Security/OutputEscapingTest.php
+++ b/tests/Security/OutputEscapingTest.php
@@ -10,7 +10,7 @@
 describe('output escaping in maint', function () {
 	it('does not interpolate raw variables into HTML attributes', function () {
 		$uiFiles = [
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		];
 
@@ -57,7 +57,7 @@
 
 	it('uses html_escape or __esc for user-controlled output', function () {
 		$uiFiles = [
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		];
 
@@ -89,7 +89,7 @@
 		// HTML hidden-input values and inline <script> URL strings in several places.
 		// Direct echoing must always go through html_escape_request_var() instead.
 		$uiFiles = [
-			'functions.php',
+			'includes/functions.php',
 			'maint.php',
 		];
 
diff --git a/tests/Security/PreparedStatementConsistencyTest.php b/tests/Security/PreparedStatementConsistencyTest.php
index d517ede..c5370f4 100644
--- a/tests/Security/PreparedStatementConsistencyTest.php
+++ b/tests/Security/PreparedStatementConsistencyTest.php
@@ -10,7 +10,7 @@
 describe('prepared statement consistency in maint', function () {
 	it('uses prepared DB helpers in all plugin files', function () {
 		$targetFiles = [
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		'setup.php',
 		];
@@ -51,7 +51,7 @@
 
 	it('uses parameterized placeholders not string interpolation in SQL', function () {
 		$targetFiles = [
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		'setup.php',
 		];
diff --git a/tests/Security/RedirectSafetyTest.php b/tests/Security/RedirectSafetyTest.php
index a48c2bf..b5fa15d 100644
--- a/tests/Security/RedirectSafetyTest.php
+++ b/tests/Security/RedirectSafetyTest.php
@@ -10,7 +10,7 @@
 describe('redirect safety in maint', function () {
 	it('calls exit or die after header Location redirects', function () {
 		$files = array(
-		'functions.php',
+		'includes/functions.php',
 		'maint.php',
 		);
 
diff --git a/tests/Unit/CheckHostTest.php b/tests/Unit/CheckHostTest.php
index 3ba263f..a3467f3 100644
--- a/tests/Unit/CheckHostTest.php
+++ b/tests/Unit/CheckHostTest.php
@@ -10,7 +10,7 @@
 uses(TestCase::class);
 
 beforeEach(function () {
-	$this->loadPluginSource('functions.php');
+	$this->loadPluginSource('includes/functions.php');
 });
 
 describe('plugin_maint_check_host type dispatch', function () {
diff --git a/tests/Unit/CheckScheduleTest.php b/tests/Unit/CheckScheduleTest.php
index 0db4b7e..20560f5 100644
--- a/tests/Unit/CheckScheduleTest.php
+++ b/tests/Unit/CheckScheduleTest.php
@@ -10,7 +10,7 @@
 uses(TestCase::class);
 
 beforeEach(function () {
-	$this->loadPluginSource('functions.php');
+	$this->loadPluginSource('includes/functions.php');
 });
 
 describe('plugin_maint_check_schedule one-time schedules', function () {
diff --git a/tests/Unit/MaintCheckUpgradeTest.php b/tests/Unit/MaintCheckUpgradeTest.php
new file mode 100644
index 0000000..17ccc11
--- /dev/null
+++ b/tests/Unit/MaintCheckUpgradeTest.php
@@ -0,0 +1,154 @@
+<?php
+/*
+ +-------------------------------------------------------------------------+
+ | Copyright (C) 2004-2026 The Cacti Group                                 |
+ +-------------------------------------------------------------------------+
+ | Cacti: The Complete RRDtool-based Graphing Solution                     |
+ +-------------------------------------------------------------------------+
+*/
+
+/*
+ * Coverage for plugin_maint_check_upgrade()'s version-change branch: driven
+ * past the page-gate with a stored plugin_config version that differs from the
+ * packaged version, it refreshes the schema (maint_upgrade_tables()) and writes
+ * the full plugin_config row.
+ */
+
+beforeAll(function () {
+	require_once __DIR__ . '/../../setup.php';
+	require_once __DIR__ . '/../../includes/database.php';
+});
+
+beforeEach(function () {
+	// Sandbox base_path (complete temp INFO + empty includes/database.php stub)
+	// so every upgrade-path test runs maint_prune_files() against a
+	// throwaway tree, never the real checkout. Tests needing a different INFO
+	// override base_path themselves.
+	$GLOBALS['__maint_base_restore'] = $GLOBALS['config']['base_path'];
+	$base = sys_get_temp_dir() . '/maint-test-' . uniqid();
+	mkdir($base . '/plugins/maint/includes', 0777, true);
+	file_put_contents($base . '/plugins/maint/INFO', "[info]\nversion = 9.9.9\nname = maint\nlongname = Maint\nauthor = x\nhomepage = x\n");
+	file_put_contents($base . '/plugins/maint/includes/database.php', "<?php\n");
+	$GLOBALS['config']['base_path'] = $base;
+});
+
+afterEach(function () {
+	if (isset($GLOBALS['__maint_base_restore'])) {
+		$GLOBALS['config']['base_path'] = $GLOBALS['__maint_base_restore'];
+	}
+});
+
+it('refreshes the schema and updates plugin_config when the stored version differs', function () {
+	/*
+	 * plugin_maint_check_upgrade() require_once's $config['library_path'] .
+	 * '/database.php' and '/functions.php' after the page-gate. The bootstrap
+	 * leaves library_path unset, so point it at a throwaway directory of empty
+	 * files to let those requires resolve without redeclaring real Cacti helpers.
+	 */
+	$lib = sys_get_temp_dir() . '/maint_lib_' . uniqid('', true);
+	mkdir($lib);
+	file_put_contents($lib . '/database.php', "<?php\n");
+	file_put_contents($lib . '/functions.php', "<?php\n");
+
+	$original_library_path             = $GLOBALS['config']['library_path'] ?? null;
+	$original_self                     = $_SERVER['PHP_SELF'] ?? null;
+	$GLOBALS['config']['library_path'] = $lib;
+
+	// Pass the page-gate: basename must be one of plugins.php / maint.php.
+	$_SERVER['PHP_SELF'] = '/cacti/plugins/maint/maint.php';
+
+	// db_table_exists defaults to false -> create branch; stale stored version.
+	$GLOBALS['__test_table_exists'] = [];
+	maint_test_queue('db_fetch_cell_prepared', '0.0-stale');
+	$GLOBALS['__test_db_calls']         = [];
+	$GLOBALS['__test_registered_hooks'] = [];
+
+	try {
+		plugin_maint_check_upgrade();
+	} finally {
+		if ($original_self === null) {
+			unset($_SERVER['PHP_SELF']);
+		} else {
+			$_SERVER['PHP_SELF'] = $original_self;
+		}
+
+		if ($original_library_path === null) {
+			unset($GLOBALS['config']['library_path']);
+		} else {
+			$GLOBALS['config']['library_path'] = $original_library_path;
+		}
+
+		@unlink($lib . '/database.php');
+		@unlink($lib . '/functions.php');
+		@rmdir($lib);
+	}
+
+	$created = array_column(array_filter($GLOBALS['__test_db_calls'], function ($call) {
+		return $call['fn'] === 'api_plugin_db_table_create';
+	}), 'sql');
+
+	$config_updates = array_filter($GLOBALS['__test_db_calls'], function ($call) {
+		return $call['fn'] === 'db_execute_prepared' && strpos($call['sql'], 'plugin_config') !== false;
+	});
+
+	$repointed = array_filter($GLOBALS['__test_registered_hooks'], function ($hook) {
+		return $hook['hook'] === 'is_device_in_maintenance' && $hook['file'] === 'includes/functions.php';
+	});
+
+	expect($created)->toContain('plugin_maint_schedules');
+	expect($created)->toContain('plugin_maint_hosts');
+	expect($repointed)->not->toBeEmpty();
+	expect($config_updates)->not->toBeEmpty();
+});
+
+it('bails out without touching the schema when the packaged INFO is incomplete', function () {
+	$lib = sys_get_temp_dir() . '/maint_lib_' . uniqid('', true);
+	mkdir($lib);
+	file_put_contents($lib . '/database.php', "<?php\n");
+	file_put_contents($lib . '/functions.php', "<?php\n");
+
+	$original_library_path             = $GLOBALS['config']['library_path'] ?? null;
+	$original_self                     = $_SERVER['PHP_SELF'] ?? null;
+	$GLOBALS['config']['library_path'] = $lib;
+	$_SERVER['PHP_SELF']               = '/cacti/plugins/maint/maint.php';
+
+	/*
+	 * plugin_maint_version() parses $config['base_path'] . '/plugins/maint/INFO'.
+	 * base_path must stay real (the require_once above reads the plugin's own
+	 * includes/database.php from it), so temporarily replace the INFO on disk
+	 * with one missing required keys to exercise the empty($info[...]) guard.
+	 */
+	$info_path   = $GLOBALS['config']['base_path'] . '/plugins/maint/INFO';
+	$info_backup = file_get_contents($info_path);
+	file_put_contents($info_path, "[info]\nname = maint\n");
+
+	$GLOBALS['__test_db_calls'] = [];
+
+	try {
+		plugin_maint_check_upgrade();
+	} finally {
+		file_put_contents($info_path, $info_backup);
+
+		if ($original_self === null) {
+			unset($_SERVER['PHP_SELF']);
+		} else {
+			$_SERVER['PHP_SELF'] = $original_self;
+		}
+
+		if ($original_library_path === null) {
+			unset($GLOBALS['config']['library_path']);
+		} else {
+			$GLOBALS['config']['library_path'] = $original_library_path;
+		}
+
+		@unlink($lib . '/database.php');
+		@unlink($lib . '/functions.php');
+		@rmdir($lib);
+	}
+
+	$config_updates = array_filter($GLOBALS['__test_db_calls'], function ($call) {
+		return $call['fn'] === 'db_execute_prepared' && strpos($call['sql'], 'plugin_config') !== false;
+	});
+
+	expect($config_updates)->toBeEmpty();
+});
diff --git a/tests/Unit/MaintDeviceActionsAndDatabaseTest.php b/tests/Unit/MaintDeviceActionsAndDatabaseTest.php
index a30c925..cd998a8 100644
--- a/tests/Unit/MaintDeviceActionsAndDatabaseTest.php
+++ b/tests/Unit/MaintDeviceActionsAndDatabaseTest.php
@@ -12,6 +12,7 @@
 
 beforeAll(function () {
 	require_once __DIR__ . '/../../setup.php';
+	require_once __DIR__ . '/../../includes/database.php';
 });
 
 beforeEach(function () {
diff --git a/tests/Unit/MaintLifecycleTest.php b/tests/Unit/MaintLifecycleTest.php
index af8b6db..a77f13d 100644
--- a/tests/Unit/MaintLifecycleTest.php
+++ b/tests/Unit/MaintLifecycleTest.php
@@ -15,6 +15,13 @@
 	require_once __DIR__ . '/../../setup.php';
 });
 
+beforeEach(function () {
+	// Keep these contract tests off the upgrade path: a non-plugin page makes
+	// plugin_maint_check_upgrade() short-circuit before the version-drift block
+	// (and its file prune), which is covered separately by MaintCheckUpgradeTest.
+	$_SERVER['PHP_SELF'] = '/graphs.php';
+});
+
 it('parses the plugin INFO file into an info array', function () {
 	$info = plugin_maint_version();
 
diff --git a/tests/Unit/PruneFilesTest.php b/tests/Unit/PruneFilesTest.php
new file mode 100644
index 0000000..97f6566
--- /dev/null
+++ b/tests/Unit/PruneFilesTest.php
@@ -0,0 +1,256 @@
+<?php
+/*
+ ex: set tabstop=4 shiftwidth=4 autoindent:
+ +-------------------------------------------------------------------------+
+ | Copyright (C) 2004-2026 The Cacti Group                                 |
+ |                                                                         |
+ | 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 2          |
+ | 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.                            |
+ +-------------------------------------------------------------------------+
+ | Cacti: The Complete RRDTool-based Graphing Solution                     |
+ +-------------------------------------------------------------------------+
+ | This code is designed, written, and maintained by the Cacti Group. See  |
+ | about.php and/or the AUTHORS file for specific developer information.   |
+ +-------------------------------------------------------------------------+
+ | http://www.cacti.net/                                                   |
+ +-------------------------------------------------------------------------+
+*/
+
+/*
+ * Unit coverage for maint_prune_files(): tombstone/tests removal,
+ * whitelist and .git protection, and logging of unaccounted-for entries.
+ */
+
+require_once __DIR__ . '/../../setup.php';
+
+function maint_prune_fixture(array $manifest): string {
+	$base   = sys_get_temp_dir() . '/maint-prune-' . uniqid();
+	$plugin = $base . '/plugins/maint';
+
+	mkdir($plugin . '/include', 0777, true);
+	file_put_contents($plugin . '/include/old.php', "<?php\n");
+	mkdir($plugin . '/tests/Unit', 0777, true);
+	file_put_contents($plugin . '/tests/Unit/SomeTest.php', "<?php\n");
+	mkdir($plugin . '/userdata', 0777, true);
+	file_put_contents($plugin . '/userdata/keep.dat', 'keep');
+	mkdir($plugin . '/includes', 0777, true);
+	file_put_contents($plugin . '/INFO', "[info]\n");
+	file_put_contents($plugin . '/setup.php', "<?php\n");
+	file_put_contents($plugin . '/oldfile.php', "<?php\n");
+	file_put_contents($plugin . '/stray.php', "<?php\n");
+	file_put_contents($plugin . '/phpunit.xml', '');
+	file_put_contents($plugin . '/.mdlrc', '');
+	file_put_contents($plugin . '/.md_style.rb', '');
+	mkdir($plugin . '/.git', 0777, true);
+	file_put_contents($plugin . '/.git/config', '');
+	file_put_contents($plugin . '/manifest.json', json_encode($manifest));
+
+	return $base;
+}
+
+beforeEach(function () {
+	$GLOBALS['__test_cacti_log'] = [];
+});
+
+it('removes tombstoned paths and the tests/ tree, keeps whitelist/.git/expected, logs strays', function () {
+	$manifest = [
+		'tombstones' => ['include/', 'oldfile.php', 'userdata/', 'gone.png'],
+		'expected'   => ['INFO', 'setup.php', 'includes/', 'manifest.json'],
+		'whitelist'  => ['userdata/'],
+	];
+
+	$base    = maint_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/maint';
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	// Tombstone and the dev-only tests/ tree are gone.
+	expect(is_dir($plugin . '/include'))->toBeFalse();
+	expect(is_dir($plugin . '/tests'))->toBeFalse();
+	expect(is_file($plugin . '/oldfile.php'))->toBeFalse();
+	expect(is_file($plugin . '/phpunit.xml'))->toBeFalse();
+
+	// Whitelisted user data, VCS metadata, and expected files are untouched.
+	// (userdata/ is even listed as a tombstone, but the whitelist wins.)
+	expect(is_file($plugin . '/userdata/keep.dat'))->toBeTrue();
+	expect(is_dir($plugin . '/.git'))->toBeTrue();
+	expect(is_file($plugin . '/INFO'))->toBeTrue();
+	expect(is_dir($plugin . '/includes'))->toBeTrue();
+	expect(is_file($plugin . '/.mdlrc'))->toBeTrue();
+	expect(is_file($plugin . '/.md_style.rb'))->toBeTrue();
+
+	// An unexpected, non-whitelisted stray is left in place but logged.
+	expect(is_file($plugin . '/stray.php'))->toBeTrue();
+
+	$logged = implode("\n", $GLOBALS['__test_cacti_log']);
+	expect($logged)->toContain('stray.php');
+	expect($logged)->not->toContain('userdata');
+	expect($logged)->not->toContain('.git');
+	expect($logged)->not->toContain('.mdlrc');
+	expect($logged)->not->toContain('.md_style.rb');
+});
+
+it('is a safe no-op when the manifest is missing', function () {
+	$base    = sys_get_temp_dir() . '/maint-prune-missing-' . uniqid();
+	mkdir($base . '/plugins/maint', 0777, true);
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	expect($GLOBALS['__test_cacti_log'])->toBe([]);
+});
+
+it('logs and skips pruning when the manifest is malformed', function () {
+	$base   = sys_get_temp_dir() . '/maint-prune-bad-' . uniqid();
+	$plugin = $base . '/plugins/maint';
+	mkdir($plugin, 0777, true);
+	file_put_contents($plugin . '/manifest.json', 'not json');
+	mkdir($plugin . '/tests', 0777, true);
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	// A malformed manifest must not delete anything.
+	expect(is_dir($plugin . '/tests'))->toBeTrue();
+	expect(implode("\n", $GLOBALS['__test_cacti_log']))->toContain('could not be parsed');
+});
+
+it('refuses to remove a tombstone that resolves outside the plugin directory', function () {
+	$manifest = [
+		'tombstones' => ['../escapee.txt'],
+		'expected'   => ['manifest.json'],
+		'whitelist'  => [],
+	];
+
+	$base    = maint_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/maint';
+	$outside = $base . '/plugins/escapee.txt';
+	file_put_contents($outside, 'precious user data');
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	// The out-of-tree file is untouched and the refusal is logged.
+	expect(is_file($outside))->toBeTrue();
+	expect(implode("\n", $GLOBALS['__test_cacti_log']))->toContain('a traversal segment');
+});
+
+it('warns when a tombstoned path cannot be removed', function () {
+	$manifest = [
+		'tombstones' => ['locked/'],
+		'expected'   => ['manifest.json'],
+		'whitelist'  => [],
+	];
+
+	$base   = maint_prune_fixture($manifest);
+	$plugin = $base . '/plugins/maint';
+	mkdir($plugin . '/locked/sub', 0777, true);
+	file_put_contents($plugin . '/locked/sub/data', 'x');
+	chmod($plugin . '/locked/sub', 0500); // read-only dir: its child cannot be unlinked
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	set_error_handler(static fn () => true); // swallow the expected unlink warning
+
+	try {
+		maint_prune_files();
+	} finally {
+		restore_error_handler();
+		$GLOBALS['config']['base_path'] = $restore;
+		@chmod($plugin . '/locked/sub', 0700);
+	}
+
+	expect(implode("\n", $GLOBALS['__test_cacti_log']))->toContain('could not remove');
+})->skip(function () {
+	return function_exists('posix_getuid') && posix_getuid() === 0;
+}, 'permission checks are bypassed for the root user');
+
+it('refuses a tombstone that escapes through a symlinked directory', function () {
+	$manifest = [
+		'tombstones' => ['escdir/secret.txt'],
+		'expected'   => ['manifest.json'],
+		'whitelist'  => [],
+	];
+
+	$base    = maint_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/maint';
+	$outside = $base . '/outside';
+	mkdir($outside, 0777, true);
+	file_put_contents($outside . '/secret.txt', 'precious user data');
+	@symlink($outside, $plugin . '/escdir');
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	// The out-of-tree file reached through the symlink is untouched and logged.
+	expect(is_file($outside . '/secret.txt'))->toBeTrue();
+	expect(implode("\n", $GLOBALS['__test_cacti_log']))->toContain('outside the plugin directory');
+})->skip(function () {
+	$probe = sys_get_temp_dir() . '/.prune-symlink-probe-' . uniqid();
+	$ok = @symlink(__FILE__, $probe);
+	@unlink($probe);
+
+	return $ok === false;
+}, 'symlinks are not supported on this filesystem');
+
+it('protects a whitelisted file from a tombstone on its parent directory', function () {
+	$manifest = [
+		'tombstones' => ['userdata/'],
+		'expected'   => ['manifest.json'],
+		'whitelist'  => ['userdata/keep.dat'],
+	];
+
+	$base    = maint_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/maint';
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		maint_prune_files();
+	} finally {
+		$GLOBALS['config']['base_path'] = $restore;
+	}
+
+	// A whitelisted file shields its parent directory from a tombstone.
+	expect(is_file($plugin . '/userdata/keep.dat'))->toBeTrue();
+});
diff --git a/tests/bin/patch-coverage.php b/tests/bin/patch-coverage.php
index e65b53d..fc06000 100644
--- a/tests/bin/patch-coverage.php
+++ b/tests/bin/patch-coverage.php
@@ -118,11 +118,16 @@ function changed_lines($base_ref) {
 	$path     = (string) $file['name'];
 	$relative = null;
 
+	// Pick the most specific (longest) matching candidate. A shorter path can
+	// be a suffix of a longer one (e.g. the root back-compat 'functions.php'
+	// shim vs 'includes/functions.php'), so a first-match would misattribute
+	// the clover file to the wrong changed path and report the real file as
+	// unmeasured.
 	foreach (array_keys($changed) as $candidate) {
 		if ($path === $candidate || substr($path, -strlen('/' . $candidate)) === '/' . $candidate) {
-			$relative = $candidate;
-
-			break;
+			if ($relative === null || strlen($candidate) > strlen($relative)) {
+				$relative = $candidate;
+			}
 		}
 	}
 
@@ -160,6 +165,9 @@ function changed_lines($base_ref) {
  * Empty by default; add entries per repository as the need arises.
  */
 $unmeasured_allowlist = [
+	'maint.php',             // web UI entry point (chdir(../../) + require auth.php); not loadable in the isolated unit process
+	'includes/database.php', // install/upgrade/drop schema bootstrap; require_once's the live Cacti library, only runs during a real install/upgrade
+	'functions.php',         // back-compat shim; only forwards to includes/functions.php for core's hard-coded snmpagent include, nothing to cover
 ];
 $unmeasured            = array_values(array_diff(array_keys($changed), array_keys($measured)));
 $unexpected_unmeasured = array_values(array_diff($unmeasured, $unmeasured_allowlist));
diff --git a/tests/bin/validate-manifest.php b/tests/bin/validate-manifest.php
new file mode 100644
index 0000000..c54fab5
--- /dev/null
+++ b/tests/bin/validate-manifest.php
@@ -0,0 +1,73 @@
+<?php
+/*
+ +-------------------------------------------------------------------------+
+ | Copyright (C) 2004-2026 The Cacti Group                                 |
+ +-------------------------------------------------------------------------+
+ | Validates that manifest.json's "expected" array matches the plugin's    |
+ | actual top-level tree, so the manifest that drives upgrade-time pruning  |
+ | cannot silently drift. tests/, phpunit.xml, .git* and .md* are          |
+ | excluded, as are whitelisted (user-data) paths. Non-zero exit on drift. |
+ +-------------------------------------------------------------------------+
+*/
+
+$root         = dirname(__DIR__, 2);
+$manifestPath = $root . '/manifest.json';
+
+if (!is_readable($manifestPath)) {
+	fwrite(STDERR, "manifest.json not found at plugin root\n");
+	exit(1);
+}
+
+$manifest = json_decode((string) file_get_contents($manifestPath), true);
+
+if (!is_array($manifest) || !isset($manifest['expected']) || !is_array($manifest['expected'])) {
+	fwrite(STDERR, "manifest.json is missing a valid 'expected' array\n");
+	exit(1);
+}
+
+$whitelist    = isset($manifest['whitelist']) && is_array($manifest['whitelist']) ? $manifest['whitelist'] : [];
+$whitelistTop = [];
+
+foreach ($whitelist as $entry) {
+	$entry = trim((string) $entry, '/');
+
+	if ($entry !== '') {
+		$whitelistTop[explode('/', $entry)[0]] = true;
+	}
+}
+
+$actual = [];
+
+foreach (scandir($root) as $entry) {
+	if ($entry === '.' || $entry === '..' || $entry === 'tests' || $entry === 'phpunit.xml') {
+		continue;
+	}
+
+	if (strncmp($entry, '.git', 4) === 0 || strncmp($entry, '.md', 3) === 0 || isset($whitelistTop[$entry])) {
+		continue;
+	}
+
+	$actual[] = is_dir($root . '/' . $entry) ? $entry . '/' : $entry;
+}
+
+$expected = $manifest['expected'];
+sort($actual);
+sort($expected);
+
+$missing = array_values(array_diff($expected, $actual));
+$extra   = array_values(array_diff($actual, $expected));
+
+if ($missing === [] && $extra === []) {
+	echo "manifest.json 'expected' matches the plugin tree.\n";
+	exit(0);
+}
+
+if ($missing !== []) {
+	fwrite(STDERR, "manifest.json lists 'expected' entries that are missing on disk:\n  " . implode("\n  ", $missing) . "\n");
+}
+
+if ($extra !== []) {
+	fwrite(STDERR, "Plugin tree has top-level entries not in manifest.json 'expected'\n(add them to 'expected', or record them under 'tombstones'/'whitelist'):\n  " . implode("\n  ", $extra) . "\n");
+}
+
+exit(1);
diff --git a/tests/bootstrap-unit.php b/tests/bootstrap-unit.php
index 81584b5..7d7bc17 100644
--- a/tests/bootstrap-unit.php
+++ b/tests/bootstrap-unit.php
@@ -203,6 +203,19 @@ function api_plugin_db_table_create($plugin, $table, $data) {
 	}
 }
 
+if (!function_exists('db_update_table')) {
+	function db_update_table($table, $data) {
+		$GLOBALS['__test_db_calls'][] = array('fn' => 'db_update_table', 'sql' => $table, 'params' => $data);
+		return true;
+	}
+}
+
+if (!function_exists('db_table_exists')) {
+	function db_table_exists($table) {
+		return $GLOBALS['__test_table_exists'][$table] ?? false;
+	}
+}
+
 $GLOBALS['__test_registered_hooks'] = array();
 
 if (!function_exists('api_plugin_register_hook')) {
@@ -270,7 +283,8 @@ function __esc($text, $domain = '') {
 
 if (!function_exists('cacti_log')) {
 	function cacti_log($message, $also_print = false, $log_type = '', $level = 0) {
-		$GLOBALS['__test_log'][] = $message;
+		$GLOBALS['__test_log'][]       = $message;
+		$GLOBALS['__test_cacti_log'][] = (string) $message;
 	}
 }