Index into vectors using integers.

This commit corrects an error that has been present since the
introduction of function wellsToSrc() in commit a50bb8f but was never
detected.  Although the conversion int->double->std::size_t is likely to
be loss-less, it is better to not introduce any more steps than are
actually needed.
Use an integer type for "maxit_" counter.

The "maxit_" counter is an upper limit on the number of non-linear
iterations in a single cell.  Declaring this as a "double" is counter
intuitive unless one expects the number to be *really* high.

Present since
  - Commit 93d4bd8 (TransportModelTwophase.hpp)
  - Commit e0d38cf (TransportModelTwophaseCompressible.hpp)
writeVector(): Avoid unneeded type conversion

std::floor() returns a double so assigning it to an int introduces a
type conversion.  There is no need to do that.  In the process, do away
with the restriction that we only write entire lines.
Reduce module prerequisites.

There is no need to include <iostream> or <fstream> when all we need is
contained in the services defined by <istream> and <ostream>.
Include <cassert> to bring in declaration of assert()
Merge pull request #162 from bska/release-cleanup

Release cleanup