Base threadloop off of ManagedThread

[charmoniumQ]

All threads that run a tight-loop and check for termination in ILLIXR should have a common base class. This eases the implementation of other features:

• Fix CPU timing infrastructure #208: Logging code can go in the common base class.
• Set thread names #222: While POSIX supports threadnames, they can only be 15 chars, which is quite restrictive. This class can support arbitrary string names. When we have advanced logging (Fix CPU timing infrastructure #208), the full name can be used from this class.

The class should support:

• In a new thread, runon_start() once, and then body() many times, and then when should_stop() becomes true, run on_stop(), and join the thread.
• get_tid()
• request_stop() triggers should_stop().
• set_name() trims the name to 15 chars (important!) and calls pthread_setname_np()

The reviewer should verify:

• The code of managed_thread is clean, followable, documented inline, and well-named.
• Likewise for Threadloop, ZED, audio_pipeline, and Switchboard.
• The documentation for plugin-authors is updated.

Note to developers: @charmoniumQ has already started this, but I haven't finished, and it's worth creating a new draft off of the new master.

• Write a new common/managed_thread.hpp based on this draft with the following changes:
  • Don't use InitProtocol. InitProtocol would simplify creation and joining without a start() and stop(), but I think it's not worth the added complexity.
  • The draft uses inheritance and virtual to define on_start(), body(), and on_stop(). This current version (in master) takes a function as a parameter to the constructor (std:function<void()>). We should go back to doing what master does, except it should be std::function<void(ManagedThread&)>, so that it can call thread.sleep and other methods.
• Use in common/threadloop.hpp (switch from std::thread to ManagedThread).
• Use in zed/src/main.cpp
• Use in audio_pipeline
• Use in common/switchboard.hpp
• Use in common/*_logger.hpp.