Fixed pore_transport by declaring rate_scaling_factor
Full implementation of Chen2007BiophysJ
Removed zero ICs for Bid and Bad from module declarations

The problem was that though having a "placeholder" initial condition for, say
tBid made it convenient to do the kinds of things that you'd want to do in the
MOMP-only case, they made it very inconvenient when you wanted to embed the
module inside a larger model. In that situation, you would have to not only
override the initial value for the Parameter (e.g. Bid_0), you would also
have to reset the initial condition pattern to be associated with full-length,
rather than truncated, Bid. Since the initial conditions that were removed
were assigned zero values, people would have to override them with some
value anyway, so it seems reasonable to force people to have to add a condition
in.

The trade-off was that the initial conditions have to be declared for those
species to show up in the reaction network, and hence to produce the ODEs that
match the test conditions. To get around this, I had to modify the setup code
for every test to add Bid_0 and/or Bad_0 initial conditions as appropriate.
Refactored pore_transport out; indirect uses aBax by default

Had to add some kludgy code to deal with the fact that some of the models use
parameters in micromolar, others in nanomolar. This should be considered
a temporary solution.
Chen2007 models all have full TRAIL implementations!
More fixes to pore_transport for shen models

Because the Cui models all use a dimeric "pore" rather than a tetramer, this required
that the shen_pore_transport macro be re-parameterized to take the pore_size as an
argument, which in turn required that the earm2.macros.pore_transport macro be
reparameterized to take the size as an argument (it had defaulted to 4).

To make the dimeric pore compatible with the dimeric species generated by pore_species,
I had to change the dimeric pore from

Bax(bf=None, s1=1, s2=2, state='A') % Bax(bf=None, s1=2, s2=1, state='A')

to

Bax(bf=None, s1=1, s2=None, state='A') % Bax(bf=None, s1=None, s2=1, state='A')

Interestingly, this changed the coefficient for the corresponding binding reaction
in the odes from being scaled by 1/2 to being scaled by 1. It turned out that this
is because, even though the binding reaction is still homomeric, because it can
happen in two ways (the Baxes can dimerize on either "side") it gets rescaled by 2,
and the two scaling factors cancel out (see comment in cui2008_direct in
shen_modules.py, below).

After making this fix, I had to edit the tested ODEs in test_shen_models.py
accordingly.
Fixed pore_transport argument to cui
Added Cui full models, but the modules should be validated
Added Howells; removed Bad initial condition from Howells
Added do_pore_assembly argument to howells
Ignore the kr_coeff_test directory in earm2
Removed Bad and Noxa (temporarily); made MATLAB for Hoda

Since setting the initial conditions to 0 doesn't remove Bad and Noxa from
the reaction network, the initial conditions had to be removed (since
Hoda should not be fitting them in this case). However even this left
the Bad and Noxa binding parameters in the parameter list, so they would
be included in the fitting procedure. So I had to comment out the sensitizer
binding step of the model. However, I plan to reinstate these elements
immediately after this commit.
Fixes to observables MATLAB file (indexes were off by 1)