base: Fix race in PollQueue and remove SIGALRM workaround

There is a race between enabling asynchronous IO for a file descriptor
and IO events happening on that descriptor. A SIGIO won't normally be
delivered if an event is pending when asynchronous IO is
enabled. Instead, the signal will be raised the next time there is an
event on the FD. This changeset simulates a SIGIO by setting the
async_io flag when setting up asynchronous IO for an FD. This causes
the main event loop to poll all file descriptors to check for pending
IO. As a consequence of this, the old SIGALRM hack should no longer be
needed and is therefore removed.

Factor code out of main.cc and main.i into a bunch of files
so things are organized in a more sensible manner. Take apart
finalInit and expose the individual functions which are now
called from python. Make checkpointing a bit easier to use.