Fix #214

* Put profiling instructions for generating profiling information for
gprof into the object or executable file.
* We don't use gprof to profile.
* Fix #212

* Produce warning messages about a number of things that are legal but
dubious.

Issue #206

Fix #206

Fix #216

Avoid to implement an empty function in generators.

* From swig documentation about java binding:
"If you are going to use optimisations turned on with gcc (for example
-O2), ensure you also compile with -fno-strict-aliasing. The GCC
optimisations have become more aggressive from gcc-4.0 onwards and will
result in code that fails with strict aliasing optimisations turned on."
* http://www.swig.org/Doc1.3/Java.html

This test check the number of samples after transcode, between input and
output media. The number of channels needs to be the same.

Cannot getFps() from nbFrames anymore. So always get fps from a compute
with timebase.

* New source folder 'reader': contains utility classes to read
video/audio/... streams.
* Add IReader class.
* Add VideoReader class.
* Update avplay app: use VideoReader class.

* readFrameAt contains the logic.
* readNextFrame and readPrevFrame call readFrameAt.

This constructor can improve performances when you create several
AudioReader from one InputFile.

* VideoReader and AudioReader instanciate specific classes (to manage
video or audio).
* Add IReader.cpp

* Implement it in AudioDecoder.
* It was already done by the VideoDecoder.

Override this method is sub-classes.

They are not accessible in subclasses.

* With the Frame object, we can access the buffer, the size, the number
of samples in case of audio frame, etc...
* Update avplay app.

…tream

Some codecs need / can use extradata like Huffman tables.
mjpeg: Huffman tables
rv10: additional flags
mpeg4: global headers (they can be in the bitstream or here)
...

Instead of a pointer (avoid NULL).

Clean the code when need to access the AVStream.

… set

* Only used if stream PTS is not set.
* OutputFile: need to set the time_base of the AVCodecContext of audio streams to be able to compute this duration.

Avoid too much warnings when "AVStream::pts is deprecated" in some
versions.

Fix #189

OutputFile: copy extradata of codec context when create a new video stream

CMake: fix double dependencies of av/sw resample

Fix output stream duration

Since it's not used/maintained (we use only Travis).

Readme: add link to doxygen doc

Need to expose these methods in avtranscoder dlls (used by avmeta application).

* Use average framerate that has come from the AVStream.
* Clean doc.

Fix get fps

From now use version numbers as follow: major.minor.patch
* major: major update
* minor: new feature / API change
* patch: fix