diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 9736814..0033eb3 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -4,7 +4,7 @@
 
 When generating code for this repository:
 
-1. **Version Compatibility**: This is a Cacti plugin (`slowlog`, version 2.1) targeting Cacti 1.2.32+
+1. **Version Compatibility**: This is a Cacti plugin (`slowlog`, version 2.1) targeting Cacti 1.2.29+
 2. **Context Files**: Prioritize patterns and standards defined in this file (`.github/copilot-instructions.md`)
 3. **Codebase Patterns**: When context files don't provide specific guidance, scan the codebase for established patterns
 4. **Architectural Consistency**: Maintain plugin-based architecture extending Cacti core
@@ -20,26 +20,26 @@ When generating code for this repository:
 ### Key Dependencies
 - Cacti core framework (`api_plugin_*`, `db_*`)
 - `js/` chart rendering for slow-query analysis views
-- `keywords.txt` reserved-word reference used by the log parser
+- `docs/keywords.txt` reserved-word reference used by the log parser
 
 ## Project Structure
 
 ```
-slowlog/                   # Repository root (install to plugins/slowlog/ in Cacti)
-├── images/                  # UI icons
-├── includes/                  # Library/helper files, require_once'd from the entry points
-│   ├── database.php             # Schema management: table defs + create/upgrade/drop helpers
-│   └── slowlog_functions.php      # Log parsing, import, and charting logic
-├── js/                            # Chart rendering client-side code
-├── locales/                         # Internationalization files
-├── tests/                             # Test suite
-├── themes/                              # CSS theme overlays
-├── import_log.php                         # CLI slow-query-log importer
-├── keywords.txt                             # SQL reserved-word list used by the parser
-├── slowlog.php                                # Main viewer/administration UI
-├── INFO                                         # Plugin metadata (name, version, compat)
+slowlog/                      # Repository root (install to plugins/slowlog/ in Cacti)
+├── images/                   # UI icons
+├── includes/                 # Library/helper files, require_once'd from the entry points
+│   ├── database.php          # Schema management: table defs + create/upgrade/drop helpers
+│   └── slowlog_functions.php # Log parsing, import, and charting logic
+├── js/                       # Chart rendering client-side code
+├── locales/                  # Internationalization files
+├── tests/                    # Test suite
+├── docs/                     # keywords.txt (SQL reserved-word list used by the parser)
+├── css/                      # CSS theme overlays
+├── import_log.php            # CLI slow-query-log importer
+├── slowlog.php               # Main viewer/administration UI
+├── INFO                      # Plugin metadata (name, version, compat)
 ├── README.md
-└── setup.php                                     # Plugin install/uninstall/upgrade hooks
+└── setup.php                 # Plugin install/uninstall/upgrade hooks
 ```
 
 ## Naming Conventions
@@ -83,7 +83,7 @@ db_execute("DELETE FROM plugin_slowlog WHERE logid = $logid");
 ```
 
 ### Log Import Handling
-`import_logfile()`/`slowlog_import()` parse arbitrary uploaded/imported slow-query-log text. Treat log contents as untrusted: never `eval()` or directly execute parsed queries, and use `keywords.txt`-driven tokenizing (`is_reserved_word()`) rather than ad hoc regex that could mis-parse crafted input.
+`import_logfile()`/`slowlog_import()` parse arbitrary uploaded/imported slow-query-log text. Treat log contents as untrusted: never `eval()` or directly execute parsed queries, and use `docs/keywords.txt`-driven tokenizing (`is_reserved_word()`) rather than ad hoc regex that could mis-parse crafted input.
 
 ### Input Validation
 Use `get_filter_request_var()` / `get_nfilter_request_var()` for request input; never read `$_GET`/`$_POST` directly.
@@ -223,3 +223,7 @@ 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, `slowlog_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 17aa76b..3f95d94 100644
--- a/.github/workflows/plugin-ci-workflow.yml
+++ b/.github/workflows/plugin-ci-workflow.yml
@@ -88,6 +88,9 @@ jobs:
     - name: Check PHP version
       run: php -v
 
+    - name: Validate plugin manifest (expected-file drift)
+      run: php cacti/plugins/slowlog/tests/bin/validate-manifest.php
+
     - name: Run apt-get update
       run: sudo apt-get update
 
diff --git a/INFO b/INFO
index d394f46..8579854 100644
--- a/INFO
+++ b/INFO
@@ -5,5 +5,5 @@ longname = MySQL/MariaDB Slow Log Viewer
 author = The Cacti Group
 email = 
 homepage = http://www.cacti.net
-compat = 1.2.32
+compat = 1.2.29
 capabilities = online_view:1, online_mgmt:1, offline_view:0, offline_mgmt:0, remote_collect:0
diff --git a/themes/modern/apexcharts.css b/css/modern_apexcharts.css
similarity index 100%
rename from themes/modern/apexcharts.css
rename to css/modern_apexcharts.css
diff --git a/keywords.txt b/docs/keywords.txt
similarity index 100%
rename from keywords.txt
rename to docs/keywords.txt
diff --git a/includes/database.php b/includes/database.php
index d2651ce..63bf23a 100644
--- a/includes/database.php
+++ b/includes/database.php
@@ -251,8 +251,8 @@ function slowlog_setup_table_new(): void {
 
 	// The (id, word) primary key doesn't prevent duplicate words on a re-run, since id is
 	// auto-incrementing - only load once, when the table is still empty.
-	if (file_exists(__DIR__ . '/../keywords.txt') && !db_fetch_cell_prepared('SELECT COUNT(*) FROM plugin_slowlog_reserved_words')) {
-		$words = file(__DIR__ . '/../keywords.txt') ?: [];
+	if (file_exists(__DIR__ . '/../docs/keywords.txt') && !db_fetch_cell_prepared('SELECT COUNT(*) FROM plugin_slowlog_reserved_words')) {
+		$words = file(__DIR__ . '/../docs/keywords.txt') ?: [];
 
 		if (cacti_sizeof($words)) {
 			foreach ($words as $word) {
diff --git a/manifest.json b/manifest.json
new file mode 100644
index 0000000..462bd23
--- /dev/null
+++ b/manifest.json
@@ -0,0 +1,23 @@
+{
+    "tombstones": [
+        "keywords.txt",
+        "themes/"
+    ],
+    "expected": [
+        "CHANGELOG.md",
+        "INFO",
+        "LICENSE",
+        "README.md",
+        "css/",
+        "docs/",
+        "images/",
+        "import_log.php",
+        "includes/",
+        "js/",
+        "locales/",
+        "manifest.json",
+        "setup.php",
+        "slowlog.php"
+    ],
+    "whitelist": []
+}
diff --git a/setup.php b/setup.php
index 5754194..1b55ab0 100644
--- a/setup.php
+++ b/setup.php
@@ -209,6 +209,8 @@ function slowlog_check_upgrade(): void {
 
 		// The schema create/refresh lives in includes/database.php (the thold model).
 		slowlog_upgrade_tables();
+
+		slowlog_prune_files();
 	}
 }
 
@@ -335,3 +337,173 @@ function slowlog_show_tab(): void {
 		}
 	}
 }
+
+/**
+ * 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 slowlog_prune_files(): void {
+	global $config;
+
+	$plugin_dir    = $config['base_path'] . '/plugins/slowlog';
+	$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: slowlog manifest.json could not be parsed; skipping file prune', false, 'SLOWLOG');
+
+		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: slowlog prune refused to remove %s: path contains a traversal segment (tampered manifest.json?)', $rel), false, 'SLOWLOG');
+
+			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: slowlog prune refused to remove %s: path resolves outside the plugin directory (tampered manifest.json?)', $rel), false, 'SLOWLOG');
+
+			continue;
+		}
+
+		if (is_dir($path) && !is_link($path)) {
+			$removed = slowlog_rmtree($path);
+		} else {
+			$removed = @unlink($path);
+		}
+
+		if (!$removed) {
+			cacti_log(sprintf('WARNING: slowlog upgrade could not remove %s (check file/directory permissions)', $rel), false, 'SLOWLOG');
+		}
+	}
+
+	// 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: slowlog upgrade found a file/directory not described in manifest.json: %s (left in place)', $entry), false, 'SLOWLOG');
+	}
+}
+
+/**
+ * Recursively deletes a directory and its contents. Symlinks are removed
+ * without being followed. Helper for slowlog_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 slowlog_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($path)) {
+			if (!slowlog_rmtree($path)) {
+				$ok = false;
+			}
+		} elseif (!@unlink($path)) {
+			$ok = false;
+		}
+	}
+
+	if (!@rmdir($dir)) {
+		$ok = false;
+	}
+
+	return $ok;
+}
diff --git a/slowlog.php b/slowlog.php
index 8041aa9..1b8a9f4 100644
--- a/slowlog.php
+++ b/slowlog.php
@@ -343,8 +343,8 @@ function slowlog_import(): void {
 
 	print get_md5_include_js('plugins/slowlog/js/apexcharts.js');
 
-	if (file_exists($config['base_path'] . "/plugins/slowlog/themes/$selected_theme/apexcharts.css")) {
-		print get_md5_include_css("plugins/slowlog/themes/$selected_theme/apexcharts.css");
+	if (file_exists($config['base_path'] . "/plugins/slowlog/css/{$selected_theme}_apexcharts.css")) {
+		print get_md5_include_css("plugins/slowlog/css/{$selected_theme}_apexcharts.css");
 	} else {
 		print '<link href="' . html_escape($config['url_path'] . 'plugins/slowlog/js/apexcharts.css') . '" type="text/css" rel="stylesheet">';
 	}
@@ -1036,8 +1036,8 @@ function slowlog_view_charts(string $method): void {
 
 	print get_md5_include_js('plugins/slowlog/js/apexcharts.js');
 
-	if (file_exists($config['base_path'] . "/plugins/slowlog/themes/$selected_theme/apexcharts.css")) {
-		print get_md5_include_css("plugins/slowlog/themes/$selected_theme/apexcharts.css");
+	if (file_exists($config['base_path'] . "/plugins/slowlog/css/{$selected_theme}_apexcharts.css")) {
+		print get_md5_include_css("plugins/slowlog/css/{$selected_theme}_apexcharts.css");
 	} else {
 		print '<link href="' . html_escape($config['url_path'] . 'plugins/slowlog/js/apexcharts.css') . '" type="text/css" rel="stylesheet">';
 	}
diff --git a/tests/Unit/PruneFilesTest.php b/tests/Unit/PruneFilesTest.php
new file mode 100644
index 0000000..f2eb1ae
--- /dev/null
+++ b/tests/Unit/PruneFilesTest.php
@@ -0,0 +1,255 @@
+<?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/                                                   |
+ +-------------------------------------------------------------------------+
+*/
+
+/*
+ * Unit coverage for slowlog_prune_files(): tombstone/tests removal,
+ * whitelist and .git protection, and logging of unaccounted-for entries.
+ */
+
+require_once __DIR__ . '/../../setup.php';
+
+function slowlog_prune_fixture(array $manifest): string {
+	$base   = sys_get_temp_dir() . '/slowlog-prune-' . uniqid();
+	$plugin = $base . '/plugins/slowlog';
+
+	mkdir($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/'],
+	];
+
+	$base    = slowlog_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/slowlog';
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		slowlog_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 () {
+	$base    = sys_get_temp_dir() . '/slowlog-prune-missing-' . uniqid();
+	mkdir($base . '/plugins/slowlog', 0777, true);
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		slowlog_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() . '/slowlog-prune-bad-' . uniqid();
+	$plugin = $base . '/plugins/slowlog';
+	mkdir($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 {
+		slowlog_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'  => [],
+	];
+
+	$base    = slowlog_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/slowlog';
+	$outside = $base . '/plugins/escapee.txt';
+	file_put_contents($outside, 'precious user data');
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		slowlog_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'  => [],
+	];
+
+	$base   = slowlog_prune_fixture($manifest);
+	$plugin = $base . '/plugins/slowlog';
+	mkdir($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 {
+		slowlog_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'  => [],
+	];
+
+	$base    = slowlog_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/slowlog';
+	$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 {
+		slowlog_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'],
+	];
+
+	$base    = slowlog_prune_fixture($manifest);
+	$plugin  = $base . '/plugins/slowlog';
+	$restore = $GLOBALS['config']['base_path'];
+
+	$GLOBALS['config']['base_path'] = $base;
+
+	try {
+		slowlog_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/Unit/SlowlogCheckUpgradeTest.php b/tests/Unit/SlowlogCheckUpgradeTest.php
index fb6062e..0f82468 100644
--- a/tests/Unit/SlowlogCheckUpgradeTest.php
+++ b/tests/Unit/SlowlogCheckUpgradeTest.php
@@ -20,6 +20,9 @@
 
 beforeAll(function () {
 	require_once __DIR__ . '/../../setup.php';
+	// Define slowlog_upgrade_tables() from the real checkout so
+	// slowlog_check_upgrade() runs while base_path is sandboxed below.
+	require_once __DIR__ . '/../../includes/database.php';
 
 	$stubLibraryPath = sys_get_temp_dir() . DIRECTORY_SEPARATOR . 'slowlog-test-lib-stub';
 
@@ -36,6 +39,24 @@
 beforeEach(function () {
 	slowlog_test_reset_db_mocks();
 	unset($_SERVER['PHP_SELF']);
+
+	// Sandbox base_path so the version-drift branch runs
+	// slowlog_prune_files() against a throwaway tree with no
+	// manifest.json (prune no-ops), never the real checkout. The temp tree
+	// carries a copy of the real INFO (so slowlog_version() still matches)
+	// and an empty includes/database.php the top-level require_once can load.
+	$GLOBALS['__slowlog_base_restore'] = $GLOBALS['config']['base_path'];
+	$base = sys_get_temp_dir() . '/slowlog-test-' . uniqid();
+	mkdir($base . '/plugins/slowlog/includes', 0777, true);
+	copy(__DIR__ . '/../../INFO', $base . '/plugins/slowlog/INFO');
+	file_put_contents($base . '/plugins/slowlog/includes/database.php', "<?php\n");
+	$GLOBALS['config']['base_path'] = $base;
+});
+
+afterEach(function () {
+	if (isset($GLOBALS['__slowlog_base_restore'])) {
+		$GLOBALS['config']['base_path'] = $GLOBALS['__slowlog_base_restore'];
+	}
 });
 
 it('does nothing on a page that does not need the version check', function () {
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  ", $extra) . "\n");
+}
+
+exit(1);
diff --git a/tests/bootstrap-unit.php b/tests/bootstrap-unit.php
index 1be1648..abe64f2 100644
--- a/tests/bootstrap-unit.php
+++ b/tests/bootstrap-unit.php
@@ -314,6 +314,8 @@ function __esc($text, ...$args) {
 
 if (!function_exists('cacti_log')) {
 	function cacti_log($message, $also_print = false, $log_type = '', $level = 0) {
+		$args = func_get_args();
+		$GLOBALS["__test_cacti_log"][] = isset($args[0]) ? (string) $args[0] : "";
 	}
 }