diff --git a/public/index.php b/public/index.php
index 1acce64..a864db4 100644
--- a/public/index.php
+++ b/public/index.php
@@ -3,8 +3,7 @@
 
 define('APP_ROOT', dirname(dirname(__FILE__)));
 
-define('CLASSES_DIR', APP_ROOT . '/src/classes');
-define('LIB_DIR', APP_ROOT . '/src/lib');
+define('SRC_DIR', APP_ROOT . '/src');
 define('STORAGE_DIR', APP_ROOT . '/storage');
 define('TEMPLATES_DIR', APP_ROOT . '/templates');
 
@@ -12,15 +11,25 @@ define('TICKS_DIR', STORAGE_DIR . '/ticks');
 define('DATA_DIR', STORAGE_DIR . '/db');
 define('DB_FILE', DATA_DIR . '/tkr.sqlite');
 
-$include_dirs = [
-    LIB_DIR,
-    CLASSES_DIR,
-];
+// Defining this in the index instead of lib/util.php
+// to avoid chicken-and-egg issues with including it
+function recursive_glob(string $pattern, string $directory): array {
+    $files = [];
+    $iterator = new RecursiveIteratorIterator(
+        new RecursiveDirectoryIterator($directory)
+    );
 
-foreach ($include_dirs as $include_dir){
-    foreach (glob($include_dir . '/*.php') as $file) {
-        require_once $file;
+    foreach ($iterator as $file) {
+        if ($file->isFile() && fnmatch($pattern, $file->getFilename())) {
+            $files[] = $file->getPathname();
+        }
     }
+
+    return $files;
+}
+
+foreach (recursive_glob('*.php', SRC_DIR) as $file) {
+    require_once $file;
 }
 
 confirm_setup();
diff --git a/src/classes/Config.php b/src/Config/Config.php
similarity index 100%
rename from src/classes/Config.php
rename to src/Config/Config.php
diff --git a/src/classes/User.php b/src/User/User.php
similarity index 87%
rename from src/classes/User.php
rename to src/User/User.php
index 95f610a..44f8975 100644
--- a/src/classes/User.php
+++ b/src/User/User.php
@@ -1,10 +1,4 @@
 <?php
-#require_once __DIR__ . '/../bootstrap.php';
-
-#confirm_setup();
-
-// Made this a class so it could be more obvious where config settings are coming from.
-// Felt too much like magic constants in other files before.
 class User {
     // properties
     public string $username;
diff --git a/src/bootstrap.php b/src/bootstrap.php
deleted file mode 100644
index 605fac1..0000000
--- a/src/bootstrap.php
+++ /dev/null
@@ -1,87 +0,0 @@
-<?php
-
-#define('APP_ROOT', dirname(__FILE__));
-#define('CLASSES_DIR', APP_ROOT . '/classes');
-#define('LIB_DIR', APP_ROOT . '/lib');
-#define('TICKS_DIR', APP_ROOT . '/storage/ticks');
-#define('DATA_DIR', APP_ROOT . '/storage/db');
-#define('DB_FILE', DATA_DIR . '/tkr.sqlite');
-
-function verify_data_dir(string $dir, bool $allow_create = false): void {
-    if (!is_dir($dir)) {
-        if ($allow_create) {
-            if (!mkdir($dir, 0770, true)) {
-                http_response_code(500);
-                echo "Failed to create required directory: $dir";
-                exit;
-            }
-        } else {
-            http_response_code(500);
-            echo "Required directory does not exist: $dir";
-            exit;
-        }
-    }
-
-    if (!is_writable($dir)) {
-        http_response_code(500);
-        echo "Directory is not writable: $dir";
-        exit;
-    }
-}
-
-// Verify that setup is complete (i.e. the databse is populated).
-// Redirect to setup.php if it isn't.
-function confirm_setup(): void {
-    $db = get_db();
-
-    // Ensure required tables exist
-    $db->exec("CREATE TABLE IF NOT EXISTS user (
-        id INTEGER PRIMARY KEY AUTOINCREMENT,
-        username TEXT NOT NULL,
-        display_name TEXT NOT NULL,
-        password_hash TEXT NOT NULL,
-        about TEXT NULL,
-        website TEXT NULL,
-        mood TEXT NULL
-    )");
-
-    $db->exec("CREATE TABLE IF NOT EXISTS settings (
-        id INTEGER PRIMARY KEY,
-        site_title TEXT NOT NULL,
-        site_description TEXT NULL,
-        base_path TEXT NOT NULL,
-        items_per_page INTEGER NOT NULL
-    )");
-
-    // See if there's any data in the tables
-    $user_count = (int) $db->query("SELECT COUNT(*) FROM user")->fetchColumn();
-    $settings_count = (int) $db->query("SELECT COUNT(*) FROM settings")->fetchColumn();
-
-    // If either table has no records and we aren't on setup.php, redirect to setup.php
-    if ($user_count === 0 || $settings_count === 0){
-        if (basename($_SERVER['PHP_SELF']) !== 'setup.php'){
-            header('Location: setup.php');
-            exit;
-        }
-    } else {
-        // If setup is complete and we are on setup.php, redirect to index.php.
-        if (basename($_SERVER['PHP_SELF']) === 'setup.php'){
-            header('Location: index.php');
-            exit;
-        }
-    };
-}
-
-function get_db(): PDO {
-    verify_data_dir(DATA_DIR, true);
-
-    try {
-        $db = new PDO("sqlite:" . DB_FILE);
-        $db->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
-        $db->setAttribute(PDO::ATTR_DEFAULT_FETCH_MODE, PDO::FETCH_ASSOC);
-    } catch (PDOException $e) {
-        die("Database connection failed: " . $e->getMessage());
-    }
-    
-    return $db;
-}