The following patch to Cilly.pm seems to fix this problem:

1993c1993
<             '-include$' => { ONEMORE => 1, TYPE => "PREPROC" },
---
>             '-include$' => { ONEMORE => 1, TYPE => "EARLY_PREPROC" },


dagr...@rockwellcollins.com wrote on 02/11/2013 09:14:33 AM:

> 
> The attached files can be compiled in gcc as: 
> 
> > gcc -c test.c -include test.h 
> 
> The same invocation of cilly, however, fails. 
> 
> The invocation of cilly: 
> 
> > cilly -c test.c -include test.h 
> 
> Results in (essentially) the following sequence of events: 
> 
> gcc -E -include test.h test.c -o tmp1.i 
> cilly.asm.exe tmp1.i --out tmp2.cil.c 
> gcc -E -include test.h tmp2.cil.c -o tmp3.cil.i 
> gcc -c -include test.h tmp3.cil.i -o test.o 
> 
>   I would suggest that neither the second (is it 
> even needed?) nor the third invocation of gcc 
> should have the "-include" directive. 
> 
>   I am using CIL 1.5.1. 
> 
> -- test.c -------------------- 
> 
> int foo(struct kernel_param *k) { 
>   return k->len; 
> } 
> 
> -- test.h -------------------- 
> 
> struct kernel_param { 
>     const char *name; 
>     enum { 
>         OPT_STR, 
>         OPT_UINT, 
>         OPT_BOOL, 
>         OPT_INVBOOL, 
>         OPT_SIZE, 
>         OPT_CUSTOM 
>     } type; 
>     void *var; 
>     unsigned int len; 
> }; 

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