Добавил namespace и зависимости

src/Database/IdGenerator.php

@@ -1,6 +1,9 @@
 <?php
 
-class Database_IdGenerator {
+namespace ctiso\Database;
+use ctiso\Database;
+
+class IdGenerator {
     private $db;
 
     function __construct(Database $db) {

src/Database/JsonInstall.php

@@ -1,11 +1,14 @@
 <?php
 //Действия с базой данных согласно json файлу.
 
-class Database_JsonInstall {
+namespace ctiso\Database;
+use ctiso\Database\Manager;
+
+class JsonInstall {
     public $db_manager;
     public $serialColumns;
 
-	public function __construct(Database_Manager $db_manager) {
+	public function __construct(Manager $db_manager) {
 		$this->db_manager = $db_manager;
 	}
 

src/Database/Manager.php

@@ -1,6 +1,12 @@
 <?php 
 
-class Database_Manager 
+namespace ctiso\Database;
+use ctiso\Database,
+    ctiso\Tools\SQLStatementExtractor,
+    ctiso\Path,
+    Exception;
+
+class Manager 
 {
     public /*.Database.*/$db;
 
@@ -36,7 +42,7 @@ class Database_Manager
     				$file = $action["source"];
                 }
 
-                $stmtList = Tools_SQLStatementExtractor::extractFile(Path::join(dirname($db_file), $file));
+                $stmtList = SQLStatementExtractor::extractFile(Path::join(dirname($db_file), $file));
                 foreach($stmtList as $stmt) {
                     $this->db->executeQuery($stmt);
                 }

src/Database/PDOStatement.php

@@ -1,6 +1,10 @@
 <?php
 
+
 namespace ctiso\Database\PDOStatement;
+use ctiso\\PDOStatement,
+    ctiso\StatementIterator,
+    PDO;
 use ctiso\Database\StatementIterator;
 
 class PDOStatement extends \PDOStatement implements \IteratorAggregate

src/Database/Statement.php

@@ -3,7 +3,10 @@
 /**
  * Класс оболочка для PDOStatement для замены Creole 
  */
-class Database_Statement 
+namespace ctiso\Database;
+use PDO;
+
+class Statement 
 {
     protected $limit = null;
     protected $offset = null;

src/Database/StatementIterator.php

@@ -1,6 +1,9 @@
 <?php
 
-class Database_StatementIterator implements Iterator
+namespace ctiso\Database;
+use PDO;
+
+class StatementIterator implements Iterator
 {
 
     private $result;