Doxygen do not document all files

[kabanek]

Hello,

I write project in zend framework and I have a problem. I tried to generate documentation for my project, but only index.php is included.

Here is my hierarchy:

|-- Doxyfile
|-- Doxyfile~
|-- index.php
|-- library
|   |-- Kcms
|   |   |-- Controller
|   |   |   `-- Action.php
|   |   |-- Core.php
|   |   |-- Helper
|   |   |   |-- Flash.php
|   |   |   |-- Text.php
|   |   |   `-- Url.php
|   |   |-- Model
|   |   |   `-- Db.php
|   |   `-- View
|   |       `-- Smarty.php
(...)

and no files in /library directory are documented. When can I specify folders where I keep source files?