These messages are rather misleading and understandably a source of confusion. Older Ubuntu versions used Libav which is a fork of the FFmpeg project. FFmpeg returned in Ubuntu 15.04 "Vivid Vervet".
The fork was basically a non-amicable result of conflicting personalities and development styles within the FFmpeg community. It is worth noting that the maintainer for Debian/Ubuntu switched from FFmpeg to Libav on his own accord due to being involved with the Libav fork.
ffmpeg vs the fake oneFor a while both Libav and FFmpeg separately developed their own version of ffmpeg.
Libav then renamed their bizarro ffmpeg to avconv to distance themselves from the FFmpeg project. During the transition period the "not developed anymore" message was displayed to tell users to start using avconv instead of their counterfeit version of ffmpeg. This confused users into thinking that FFmpeg (the project) is dead, which is not true. A bad choice of words, but I can't imagine Libav not expecting such a response by general users.
This message was removed upstream when the fake "ffmpeg" was finally removed from the Libav source, but, depending on your version, it can still show up in Ubuntu because the Libav source Ubuntu uses is from the ffmpeg-to-avconv transition period.
In June 2012, the message was re-worded for the package libav - 4:0.8.3-0ubuntu0.12.04.1. Unfortunately the new "deprecated" message has caused additional user confusion.
Starting with Ubuntu 15.04 "Vivid Vervet", FFmpeg's ffmpeg is back in the repositories again.
To further complicate matters, Libav chose a name that was historically used by FFmpeg to refer to its libraries (libavcodec, libavformat, etc). For example the libav-user mailing list, for questions and discussions about using the FFmpeg libraries, is unrelated to the Libav project.
If you are using avconv then you are using Libav. If you are using ffmpeg you could be using FFmpeg or Libav. Refer to the first line in the console output to tell the difference: the copyright notice will either mention FFmpeg or Libav.
Secondly, the version numbering schemes differ. Each of the FFmpeg or Libav libraries contains a version.h header which shows a version number. FFmpeg will end in three digits, such as 57.67.100, and Libav will end in one digit such as 57.67.0. You can also view the library version numbers by running ffmpeg or avconv and viewing the console output.
ffmpegThe real ffmpeg is in the repository, so you can install it with:
apt-get install ffmpeg
Your options are:
ffmpeg,ffmpeg,These methods are non-intrusive, reversible, and will not interfere with the system or any repository packages.
Another possible option is to upgrade to Ubuntu 15.04 "Vivid Vervet" or newer and just use ffmpeg from the repository.
For an interesting blog article on the situation, as well as a discussion about the main technical differences between the projects, see The FFmpeg/Libav situation.