Fix disaster while making cross junction tracking optional.

This disaster was introduced in fece8cc8

When doing `bst build --track`, we were:

  o first scheduling every element to be tracked

  o later filtering out the cross junction elements

  o finally asserting consistency state, which would trigger
    an error because we previously scheduled for tracking.

Fixed this by moving all code which resolves elements to track
into Pipeline.initialize(), and removing special element list handling
from the individual build/fetch/track commands.