diff --git a/bin/cleanup.php b/bin/cleanup.php
new file mode 100644
index 0000000..0bd2228
--- /dev/null
+++ b/bin/cleanup.php
@@ -0,0 +1,166 @@
+<?php
+
+require_once('../config/dmsDefaults.php');
+require_once(KT_LIB_DIR . '/config/config.inc.php');
+require_once(KT_LIB_DIR . '/browse/browseutil.inc.php');
+
+$oConfig =& KTConfig::getSingleton();
+$fsPath = $oConfig->get('urls/documentRoot');
+
+$aIgnore = array(
+    '.', '..',
+    'CVS',
+    '.empty',
+    '.htaccess',
+    '.cvsignore',
+);
+
+$aFoldersToRemove = array();
+$aFilesToRemove = array();
+$aRepoDocumentProblems = array();
+$aRepoFolderProblems = array();
+$aRepoVersionProblems = array();
+
+function checkFileVersion($path, $version) {
+    $fod = KTBrowseUtil::folderOrDocument($path);
+    if ($fod === false) {
+        // No document by that name, so no point checking version
+        // information.
+        return;
+    }
+    return true;
+}
+
+function checkFile($path, $first = true) {
+    $pattern = "/^(.*)-((?:\d+)\.(?:\d+))$/";
+    if (preg_match($pattern, $path, $matches)) {
+        if (checkFileVersion($matches[1], $matches[2])) {
+            // If it's a version, then don't check for full path
+            // below...
+            return;
+        }
+    }
+    $fod = KTBrowseUtil::folderOrDocument($path);
+    if ($fod === false) {
+        $GLOBALS["aFilesToRemove"][] = $path;
+        return;
+    }
+}
+
+function checkDirectory($path) {
+    global $fsPath, $aIgnore;
+    $fullpath = sprintf("%s/%s", $fsPath, $path);
+
+    if (!is_dir($fullpath)) {
+        print "Not a directory: $fullpath\n";
+    }
+
+    if ($path === '/Deleted') {
+        // Deleted files handled separately.
+        return;
+    }
+
+    if (!empty($path)) {
+        $fod = KTBrowseUtil::folderOrDocument($path);
+        if ($fod === false) {
+            $GLOBALS["aFoldersToRemove"][] = $path;
+            return;
+        }
+    }
+    
+    $dh = @opendir($fullpath);
+    if ($dh === false) {
+        print "Could not open directory: $fullpath\n";
+    }
+    while (($filename = readdir($dh)) !== false) {
+        if (in_array($filename, $aIgnore)) { continue; }
+        $subrelpath = sprintf("%s/%s", $path, $filename);
+        $subfullpath = sprintf("%s/%s", $fsPath, $subrelpath);
+        if (is_dir($subfullpath)) {
+            checkDirectory($subrelpath);
+        }
+        if (is_file($subfullpath)) {
+            checkFile($subrelpath);
+        }
+    }
+}
+
+function checkRepoFolder($oFolder) {
+    global $fsPath, $aRepoFolderProblems;
+    $sFolderPath = sprintf("%s/%s", $oFolder->getFullPath(), $oFolder->getName());
+    $sFullPath = sprintf("%s/%s", $fsPath, $sFolderPath);
+    if (!is_dir($sFullPath)) {
+        $aRepoFolderProblems[] = $sFolderPath;
+    }
+}
+
+function checkRepoDocument($oDocument) {
+    global $fsPath, $aRepoDocumentProblems;
+    $sDocumentPath = $oDocument->getStoragePath();
+    $sFullPath = sprintf("%s/%s", $fsPath, $sDocumentPath);
+    if (!is_file($sFullPath)) {
+        $aRepoDocumentProblems[] = $sDocumentPath;
+    }
+    checkRepoVersions($oDocument);
+}
+
+function checkRepoVersions($oDocument) {
+    global $fsPath, $aRepoVersionProblems;
+    $table = "document_transactions";
+    $aVersions = DBUtil::getResultArrayKey(array("SELECT DISTINCT version FROM $table WHERE document_id = ?", array($oDocument->getID())), "version");
+    foreach($aVersions as $sVersion) {
+        if ($sVersion == $oDocument->getVersion()) {
+            continue;
+        }
+        $sDocumentPath = $oDocument->getStoragePath();
+        $sFullPath = sprintf("%s/%s-%s", $fsPath, $sDocumentPath, $sVersion);
+        if (!is_file($sFullPath)) {
+            $aRepoVersionProblems[] = array($sDocumentPath, $sVersion);
+            continue;
+        }
+    }
+}
+
+checkDirectory("");
+
+print "\n";
+print "Would remove these folders (and all their contents):\n";
+foreach ($aFoldersToRemove as $path) {
+    print "\t$path\n";
+}
+print "\n";
+print "Would remove these files:\n";
+foreach ($aFilesToRemove as $path) {
+    print "\t$path\n";
+}
+print "\n";
+
+$aFolders =& Folder::getList();
+foreach ($aFolders as $oFolder) {
+    checkRepoFolder($oFolder);
+}
+
+print "These folders are not on the filesystem:\n";
+foreach ($aRepoFolderProblems as $path) {
+    print "\t$path\n";
+}
+
+$aDocuments =& Document::getList(array("status_id = ?", array(LIVE)));
+foreach ($aDocuments as $oDocument) {
+    checkRepoDocument($oDocument);
+}
+print "\n";
+
+print "These documents are not on the filesystem:\n";
+foreach ($aRepoDocumentProblems as $path) {
+    print "\t$path\n";
+}
+print "\n";
+
+print "These documents have versions not on the filesystem:\n";
+foreach ($aRepoVersionProblems as $path) {
+    list($path, $version) = $path;
+    print "\t$path - version $version\n";
+}
+print "\n";
+