Lets see if I got this correctly:

1. XSUB.h is included in line 745 of pwiz_swigbindings_wrap.cxx, defining typedef struct cv CV and macro XS.
2. cv.hpp is included in line 1862 of pwiz_swigbindings_wrap.cxx, defining a different struct CV.
3. the XS macro from Perl is used first in line 2149 of pwiz_swigbindings_wrap.cxx

It is ugly, but the preprocessor can help to move the conflicting identifiers around. To do so I would manually modify the file pwiz_swigbindings_wrap.cxx and insert this line before
#define CV __perl_CV
and these ones after
#undef XSPROTO
#define XSPROTO(name) void name(pTHX_ __perl_CV* cv)
#undef CV
line 745.

#define CV __perl_CV
/* beginning of include XSUB.h */
struct cv {
        int i;
};
typedef struct cv CV;
#define XSPROTO(name) CV name
/* end of include XSUB.h */
#undef XSPROTO
#define XSPROTO(name) __perl_CV name
#undef CV

struct CV {
        char c;
};

XSPROTO(x);

int main()
{
        struct CV y;
        x.i = 0;
        y.c = '!';
        return 0;
}
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Thanks for the reply. This is all black magic to me (plus I think some newlines got lost in the code in your first paragraph) so I'm not sure if I got it right. Here is what I tried around the section you suggested:

#include "EXTERN.h"
#include "perl.h"
#define CV __perl_CV
#include "XSUB.h"
#undef XSPROTO
#define XSPROTO(name) void name(pTHX_ __perl_CV* cv)
#undef CV
[download]

That's just copying what you wrote and guessing at the newlines, so I'm not sure if the syntax is correct. If I try to compile this, the STDERR is down to ~ 1500 lines with a lot of messages like this:

pwiz_swigbindings_wrap.cxx:748:39: error: ‘__perl_CV’ has not been dec
+lared
 #define XSPROTO(name) void name(pTHX_ __perl_CV* cv)
[download]

My error, sorry. I should have said to put the line

#define CV __perl_CV

before this one

#include "perl.h"

otherwise it looks ok.

Update: some explanations added

What I intend to do, is this:

1. for the processing of perl.h, XSUB.h and the included header files therein, substitute the offending identifier CV by __perl_CV. This is done by the preprocessor directive #define CV __perl_CV
2. Afterwards redeclare the macro XSPROTO, which was using CV also. Unfortunately the above substitution affects only C code, but not subsequent preprocessor directives, so we need to adjust this macro definition.
   This is done by first deleting the old macro definition (#undef XSPROTO), and then by defining it again, but this time with __perl_CV instead of CV.
3. Finally delete the substitution for identifier CV (#undef CV, so that the following code can use it exclusively.
4. This in total should remove the conflict between the two different definitions of CV by using __perl_CV for the first one instead.

If you are curious, you can look at the difference of the preprocessed outputs with and without the modification (gcc -E -dDfile should produce them).