Minor documentation fixes:

- disabled OPTIMIZE_OUTPUT_JAVA
- filtered out *.m scripts
- removed link to old Sphinx documentation
- replaced all mentions of Sphinx with Doxygen

doc/Doxyfile.in

@@ -41,7 +41,7 @@ ALIASES               += next_tutorial{1}="**Next  Tutorial:** \ref \1 \n"
 ALIASES               += youtube{1}="@htmlonly[block]<div align='center'><iframe title='my title' width='560' height='349' src='http://www.youtube.com/embed/\1?rel=0' frameborder='0' align='middle' allowfullscreen></iframe></div>@endhtmlonly"
 TCL_SUBST              =
 OPTIMIZE_OUTPUT_FOR_C  = NO
-OPTIMIZE_OUTPUT_JAVA   = YES
+OPTIMIZE_OUTPUT_JAVA   = NO
 OPTIMIZE_FOR_FORTRAN   = NO
 OPTIMIZE_OUTPUT_VHDL   = NO
 EXTENSION_MAPPING      =
@@ -106,7 +106,7 @@ FILE_PATTERNS          =
 RECURSIVE              = YES
 EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = *.inl.hpp *.impl.hpp *_detail.hpp */cudev/**/detail/*.hpp
+EXCLUDE_PATTERNS       = *.inl.hpp *.impl.hpp *_detail.hpp */cudev/**/detail/*.hpp *.m
 EXCLUDE_SYMBOLS        = cv::DataType<*> int void
 EXAMPLE_PATH           = @CMAKE_DOXYGEN_EXAMPLE_PATH@
 EXAMPLE_PATTERNS       = *

doc/DoxygenLayout.xml

@@ -17,7 +17,6 @@
       <tab type="globals" visible="yes" title="Global objects" intro=""/>
     </tab>
     <tab type="examples" visible="yes" title="" intro=""/>
-    <tab type="user" url="/3.0-last-rst" title="Sphinx Documentation"/>
   </navindex>
 
   <!-- Layout definition for a class page -->

doc/py_tutorials/py_setup/py_setup_in_fedora/py_setup_in_fedora.markdown

@@ -102,13 +102,10 @@ yum install eigen3-devel
 @endcode
 If you want to build **documentation** ( *Yes, you can create offline version of OpenCV's complete
 official documentation in your system in HTML with full search facility so that you need not access
-internet always if any question, and it is quite FAST!!!* ), you need to install **Sphinx** (a
+internet always if any question, and it is quite FAST!!!* ), you need to install **Doxygen** (a
-documentation generation tool) and **pdflatex** (if you want to create a PDF version of it). ( Also
+documentation generation tool).
-while configuring installation with CMake, don't forget to pass -D BUILD_DOCS=ON. More details
-below.)
 @code{.sh}
-yum install python-sphinx
+yum install doxygen
-yum install texlive
 @endcode
 ### Downloading OpenCV
 
@@ -174,6 +171,7 @@ setup you got, make sure that following fields are filled (below is the some imp
 configuration I got). These fields should be filled appropriately in your system also. Otherwise
 some problem has happened. So check if you have correctly performed above steps.
 @code{.sh}
+...
 --   GUI:
 --     GTK+ 2.x:                    YES (ver 2.24.19)
 --     GThread :                    YES (ver 2.36.3)
@@ -205,15 +203,7 @@ some problem has happened. So check if you have correctly performed above steps.
 --     numpy:                       /usr/lib/python2.7/site-packages/numpy/core/include (ver 1.7.1)
 --     packages path:               lib/python2.7/site-packages
 
---   Documentation:
+...
---     Build Documentation:         YES
---     Sphinx:                      /usr/bin/sphinx-build (ver 1.1.3)
---     PdfLaTeX compiler:           /usr/bin/pdflatex
---
---   Tests and samples:
---     Tests:                       NO
---     Performance tests:           NO
---     C/C++ Examples:              NO
 @endcode
 Many other flags and settings are there. It is left for you for further exploration.
 

doc/tutorials/introduction/windows_install/windows_install.markdown

@@ -85,11 +85,8 @@ of them, you need to download and install them on your system.
     image file format.
 -   The OpenNI Framework contains a set of open source APIs that provide support for natural interaction with devices via methods such as voice command recognition, hand gestures, and body
     motion tracking. Prebuilt binaries can be found [here](http://structure.io/openni). The source code of [OpenNI](https://github.com/OpenNI/OpenNI) and [OpenNI2](https://github.com/OpenNI/OpenNI2) are also available on Github.
--   [Miktex]( http://miktex.org/2.9/setup) is the best [TEX](https://secure.wikimedia.org/wikipedia/en/wiki/TeX) implementation on
+-   [Doxygen](http://www.stack.nl/~dimitri/doxygen/) is a documentation generator and is the tool that will actually create the
-    the Windows OS. It is required to build the *OpenCV documentation*.
+    *OpenCV documentation*.
--   [Sphinx](http://sphinx.pocoo.org/) is a python documentation generator and is the tool that will actually create the
-    *OpenCV documentation*. This on its own requires a couple of tools installed, We will cover this
-    in depth at the @ref tutorial_windows_install_sphinx "How to Install Sphinx" section.
 
 Now we will describe the steps to follow for a full build (using all the above frameworks, tools and
 libraries). If you do not need the support for some of these you can just freely skip this section.
@@ -122,36 +119,10 @@ libraries). If you do not need the support for some of these you can just freely
         couple other python extensions. Luckily installing all these may be automated by a nice tool
         called [Setuptools](http://pypi.python.org/pypi/setuptools#downloads). Download and install
         again.
-        @anchor tutorial_windows_install_sphinx
-    -#  Installing Sphinx is easy once you have installed *Setuptools*. This contains a little
-        application that will automatically connect to the python databases and download the latest
-        version of many python scripts. Start up a command window (enter *cmd* into the windows
-        start menu and press enter) and use the *CD* command to navigate to your Python folders
-        Script sub-folder. Here just pass to the *easy_install.exe* as argument the name of the
-        program you want to install. Add the *sphinx* argument.
-
-        ![](images/cmsdstartwindows.jpg)
-
-        ![](images/Sphinx_Install.png)
-
-        @note
-        The *CD* navigation command works only inside a drive. For example if you are somewhere in the
-        *C:* drive you cannot use it this to go to another drive (like for example *D:*). To do so you
-        first need to change drives letters. For this simply enter the command *D:*. Then you can use
-        the *CD* to navigate to specific folder inside the drive. Bonus tip: you can clear the screen by
-        using the *CLS* command.
-
-        This will also install its prerequisites [Jinja2](http://jinja.pocoo.org/docs/) and
-        [Pygments](http://pygments.org/).
 
     -#  The easiest way to install Numpy is to just download its binaries from the [sourceforge page](http://sourceforge.net/projects/numpy/files/NumPy/).
         Make sure your download and install
         exactly the binary for your python version (so for version `2.7`).
-    -#  Download the [Miktex](http://miktex.org/2.9/setup) and install it. Again just follow the wizard. At the fourth step make
-        sure you select for the *"Install missing packages on-the-fly"* the *Yes* option, as you can
-        see on the image below. Again this will take quite some time so be patient.
-
-        ![](images/MiktexInstall.png)
 
     -#  For the [Intel Threading Building Blocks (*TBB*)](http://threadingbuildingblocks.org/file.php?fid=77)
         download the source files and extract
@@ -291,12 +262,9 @@ libraries). If you do not need the support for some of these you can just freely
 
     ![](images/OpenCVBuildResultWindows.jpg)
 
-    For the documentation, you need to explicitly issue the build commands on the *doc* project for
+    For the documentation, you need to explicitly issue the build commands on the *doxygen* project for
-    the PDF files and on the *doc_html* for the HTML ones. Each of these will call *Sphinx* to do
+    the HTML docuementation. It will call *Doxygen* to do
-    all the hard work. You can find the generated documentation inside the `Build/Doc/_html` for the
+    all the hard work. You can find the generated documentation inside the `build/doc/doxygen/html`.
-    HTML pages and within the `Build/Doc` the PDF manuals.
-
-    ![](images/WindowsBuildDoc.png)
 
     To collect the header and the binary files, that you will use during your own projects, into a
     separate directory (simillary to how the pre-built binaries ship) you need to explicitly build