[all] Port everything to Pinocchio 2.1 and to new SOT files, fix #48

This PR solves #48 (closed). With this PR, we are now using Piocchio 2.1. Also, we are now systematically using the new functionalities integrated in sot-core and in dynamic-graph. The local copies were removed.

List of changes:

• changed se3 namespace to pinocchio
• minor algorithm signature changes due to Pinocchio 2.0
• the macros contained in dynamic-graph/signal-helper.h have changed. Now, thy are adding m_ to the signal variables by default. I updated those files which were already using dynamic-graph/signal-helper.h.
• removed utils/logger.hh and corresponding src/utils/logger.cpp. Removed corresponding #include in all source files, as all entities are now endowed by default with their own logger. Removed sendMsg function from all entities, for the same reason.
• removed utils/vector-conversions.hh. Replaced it with sot-core/matrix-geometry.hh
• removed utils/signal-helper.hh. Replaced it with dynamic-graph/signal-helper.h
• removed stc-commands.hh. I have no idea why this file was there, it was not used anywhere
• removed common.hh and corresponding common.cpp. This file was not even appearing in the CMakeLists.txt, it should have been removed earlier
• removed robot-utils.hh and robot-utils.cpp, as they are in sot-core (it was not used anywhere and it was not appearing in the CMakeLists.txt)

Additionally, I removed most references to

• utils/commands-helper.hh because I think it should be removed and its functionalities should be put in dynamic-graph. Everybody is encouraged to use <dynamic-graph/all-commands.hh>, unless you really know you need something inside commands-helper.hh