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I'm running OS X 10.6.5 and Xcode 3.2.5 (1760). I just downloaded a fresh install [sage-4.6-OSX-64bit-10.6-i386-Darwin.dmg], copied the volume into /Applications in the usual way, and installed sage-mode. Cloning worked for me:

localhost:sage mcneil$ ./sage -clone local_mod
Now cloning the current Sage library branch...
hg clone  sage sage-local_mod 
updating working directory
2339 files updated, 0 files merged, 0 files removed, 0 files unresolved
Copying over all Cython auto-generated .c, .cpp and .h files...
Copying over build directory...
Copying over all auto-generated reference manual .rst files...
Copying over documentation output...
Building sage-local_mod...
sage -b local_mod

sage: Building and installing modified Sage library files.

Installing c_lib
gcc -o src/convert.os -c -fPIC -I/Applications/sage/local/include -I/Applications/sage/local/include/python2.6 -I/Applications/sage/local/include/NTL -Iinclude src/convert.c


I think the key is figuring out why it can't find your stdlib.h. The corresponding line in pari.h is #include <stdlib.h>, so it should pick up from the environment. By inserting garbage into /usr/include/stdlib.h and forcing a rebuild I confirmed that's the one it's using for me (and not one of the SDK versions it noticed). Could you check the existence and permissions of /usr/include/stdlib.h as well as your environment variables? What include paths does your gcc use?