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Replies to Referee A
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1) The compressed scale in Fig.2 in the paper makes the quantitative
analysis of the data quite difficult. I much prefered the way the data
were presented at the DNP fall meeting and the QM conference. But after
careful checking I conclude that the data in the paper and the data
shown at the conferences are consistent. So this is just my preference
regarding plotsmanship and it should be taken as a suggestion.

In order for the figures to be useful quantitatively they would have to be much larger with the consequence of taking substantial space from the text. However, the spectra and ratios shown in the paper are available as numerical tables on the BRAHMS web page under the Publication section.

2.) I think the paper should clearly state the pseudo-rapidity bins
that were used for the measurements rather than saying 'narrow intervals
around eta = 0,1,2.2,3.2'. How narrow ? And how does the narrowness
affect the statistics ?

Figure 1 shows the eta intervals with dotted lines. The value of that interval is 0.2 at eta=0 and 1, 0.25 at eta=2.2 and equal to 0.45 at eta=3.2

We have added a sentence to the text (see item 4 in Summary of Changes).

The acceptance of the spectrometers and the beam luminosity are reflected in the statistical errors shown and the eta and pt bin sizes used.  The main consequence of this limitation is to restrict the pt reach.
  
3.) What are the different colored contours in the upper row of Fig.1 ?
They are neither explained in the text nor the figure caption.

The figures in the upper row of Fig. 1 show the outline of the data sample for specific magnetic field settings, the first panel (eta=0) shows two field settings, the second panel (eta=1) shows a single field setting, at eta = 2.2 we used three settings, and at 3.2 we used two field settings.  Whenever the outlines overlap, the line color has been changed to gray.  An explanatory line has been added to the caption of figure 1, indicated in item 5 of the Summary of Changes.

4) Fig.6 top: 'based on simulations the ratios calculated with negative
particles are larger in forward rapidities than the ones calculated with
the charge average.' Why ? By how much ? Is that in the systematic error? 
Could it be corrected on the basis of the simulations ? Has that been
done for the data presented here ? 

This sentence was included to acknowledge a current discussion within the collaboration as to the correct way to make the ratio RdAu taking into account the isospin of both numerator and denominator. What we want to state is that by making the ratio with the negative particles we obtain a value greater than the one that would be extracted using  the average charge of the outgoing particles.  To estimate the difference if the ratios were calculated with average charge, we simulated the yield of positive particles from p+p at eta = 3.2 using HIJING. With that information and with our measured positives from d+Au, we can state that at pt=2 GeV/c the ratio of the RdAu ratio constructed with   (h+ + h-)/2 would be ~1.7 times smaller than the one presented in the paper.

Why?

In p+p collisions there is a small excess of  positive pions  at forward rapidities  and at pt higher than ~1 GeV/c, protons and positive kaons make a significant difference.

Could it be corrected?

Yes but we decided against that correction to avoid the inclusion of model dependent simulated spectra. The data has no corrections for that difference.

5.) Fig.6 middle: 'strong correlation between ratio of charge particle
eta densities and R(dA) values.' What does that mean ? Maybe one
sentence of explanation should be added here and not just two
references. What are the physics implications ? And how strong is that
correlation ? It seems correlation in this context is defined as the
fact that the R(dA) values in the lowest pt bin shown here reach the
dashed line. Well, the lowest pt bin shown varies from eta-bin to
eta-bin. Is there a claim that the R(dA) values would be constant below
the lowest measured bin and therefore follow the density ratio line ? Is
this an indirect argument for participant scaling at low pt ? Please add
a sentence about the physics relevance of this agreement between R(dA)
and particle density ratio.

When we wrote the manuscript it was observed that a similar change with eta was seen in the ratio of the multiplicity densities.  Since the magnitude of this density is mainly driven by the low pt events, that effect would be related to the so called soft-physics. We included this sentence simply as an experimental observation confirmed by two independent measurements. The text has been changed as in item 8 of the Summary of Changes.  
The ratio obtained from the multiplicity densities is not a function of pt.  We have displayed this ratio with dashed lines extending to 1 GeV/c mainly to let it stand out in the figures. It is not our intention to indicate that the RdAu should then follow that constant behavior.  We have changed the last paragraphs of the Letter as indicated in item 10 of the Summary of Changes.

6.) Fig.7 end of first paragraph: 'the functional form of the c-to-p
ratio is close to that of the saturation scale.' Which functional form
of the saturation scale ? The one shown on page 3: Q**2 prop. e(Lambda
y) ?  So Lambda is 0.2-0.3 based on HERA data and alpha on page 7 is
-0.28 based on BRAHMS data. Is that the connection ? Please elaborate by
adding one sentence of explanation. Also, the saturation scale in HERA
is measured in rapidity not in pseudorapidity. Wouldn't that cause a
difference to the functional form at very forward rapidities ?

Yes we found interesting that the Rcp from our sample of central events averaged from 2.5 to 4.0 GeV/c has the same rapidity dependence as the saturation scale Qs2 shown in page 3. We state at the end of the paragraph that this similarity only appears for central events. 
We know now that at eta = 2.2, 70% of the negative charged particles are pions and at eta = 3.2 HIJING gives 83%.  We also make use of the fact that for pions, pseudo-rapidity is practically equal to rapidity, and we can use both quantities interchangeably.

The end of this paragraph is now modified to clarify this connection between our results and HERA’s as in item 9 of the Summary of Changes.

7.) Fig.8 in the summary: a.) 'results are consistent with a
modification of the Gold wave function'. I am not sure whether the 'Gold
wave function' here is not too generic a term. I am not really sure what
the authors mean by modification to the Gold wave function. 

The use of the term "Gold wave function" in the context of this paper refers to a description of the gold ion at the parton level, something like a Parton Distribution Function for the entire gold nuclei. We changed that statement as listed in item 10 of the Summary of Changes.
   
  b.) next sentence: 'such modifications produced a suppression at all values of pt
similar to the multiplicity density ratio.' So this goes even further
than the statement in the text to Fig.2 where it was stated that the
R(dA) values reach the particle density ratios at low pt. Here now the
modifications is the same for all pt's. I guess this relates to the
solid symbols in the last panel of Fig.3. Again, the relation between
particle density and suppression factor is not explained. Is the fact
that for this bin the R(dA) are near constant an indication of an
initial state effect ? How does this relate to the statement in the text
   about Fig.2 ?.

b) As we said in our reply to your point 5, we are only reporting the experimental observation: the RdAu ratios at pt close to 0 have roughly the same value as the ones calculated from the multiplicity densities. We understand that the language used in the paper seems to indicate some physics predilection.  In order to avoid this bias we have changed the text in two places as indicated in items 8 and 10 of the Summary of Changes.  According to the CGC theory, as the rapidity of the detected particles gets closer to the deuteron rapidity, the rate of gluon fusion in the Au ion slows the growth of the gluon density compared with the that of the p+p system where gluon fusion is not expected..  However, the change of the RdAu ratio as function of rapidity is not necessarily the same at all pts. 

c.) I think the final sentence of the paper should be
taken out because it states a preference in the interpretation of the
data that can not yet be unambiguously corroborated. The paper nicely
states the alternate HIJING based approach that utilizes increased gluon
shadowing. Maybe the difference between color glass condensate and
strong gluon shadowing is just semantics, but I would not claim evidence
for gluon saturation on the basis of this measurement alone. The data
are very exciting in their own right and do not require a statement by
the experimentalists on the ongoing model controversy

  We have changed that sentence so as not to lead the reader to think that our results do settle the ongoing model controversy. Please see item 10 of the Summary of Changes.