For reference, here's what I got last night on Linux after a make realclean, svn up and perl Configure.pl.
$ make headerizer && make /usr/local/bin/perl tools/build/headerizer.pl src/string.o src/ops/core_ops.o src/ops/core_ops_switch.o src/atomic/gcc_x86.o src/builtin.o src/byteorder.o src/charset.o src/core_pmcs.o src/cpu_dep.o src/datatypes.o src/debug.o src/dynext.o src/embed.o src/encoding.o src/events.o src/exceptions.o src/exit.o src/extend.o src/extend_vtable.o src/gc/dod.o src/gc/gc_gms.o src/gc/gc_ims.o src/gc/memory.o src/gc/register.o src/gc/smallobject.o src/global.o src/global_setup.o src/hash.o src/headers.o src/hll.o src/inter_call.o src/inter_cb.o src/inter_create.o src/inter_misc.o src/interpreter.o src/inter_run.o src/intlist.o src/key.o src/library.o src/list.o src/longopt.o src/misc.o src/mmd.o src/nci.o src/oo.o src/packfile.o src/packout.o src/pic_jit.o src/pic.o src/platform.o src/pmc_freeze.o src/pmc.o src/runops_cores.o src/scheduler.o src/spf_render.o src/spf_vtable.o src/stacks.o src/stm/backend.o src/stm/waitlist.o src/string_primitives.o src/sub.o src/thread.o src/trace.o src/tsq.o src/utils.o src/vtables.o src/warnings.o src/packfile/pf_items.o src/ops/core_ops_cg.o src/ops/core_ops_cgp.o src/exec.o src/exec_cpu.o src/exec_dep.o src/exec_save.o src/jit.o src/jit_cpu.o src/jit_debug.o src/jit_debug_xcoff.o src/gc/resources.o src/charset/ascii.o src/charset/binary.o src/charset/iso-8859-1.o src/charset/tables.o src/charset/unicode.o src/io/io.o src/io/io_buf.o src/io/io_layers.o src/io/io_unix.o src/io/io_utf8.o src/io/io_mmap.o src/io/io_win32.o src/io/io_stdio.o src/io/io_string.o src/io/io_passdown.o src/pmc/default.o src/pmc/null.o src/pmc/env.o src/pmc/key.o src/pmc/random.o src/pmc/unmanagedstruct.o src/pmc/managedstruct.o src/pmc/delegate.o src/pmc/exception.o src/pmc/vtablecache.o src/pmc/parrotio.o src/pmc/parrotlibrary.o src/pmc/parrotinterpreter.o src/pmc/parrotthread.o src/pmc/lexpad.o src/pmc/timer.o src/pmc/pointer.o src/pmc/sub.o src/pmc/closure.o src/pmc/continuation.o src/pmc/retcontinuation.o src/pmc/coroutine.o src/pmc/eval.o src/pmc/nci.o src/pmc/float.o src/pmc/integer.o src/pmc/bigint.o src/pmc/complex.o src/pmc/string.o src/pmc/boolean.o src/pmc/ref.o src/pmc/sharedref.o src/pmc/array.o src/pmc/fixedintegerarray.o src/pmc/intlist.o src/pmc/iterator.o src/pmc/sarray.o src/pmc/fixedstringarray.o src/pmc/multiarray.o src/pmc/hash.o src/pmc/orderedhash.o src/pmc/tqueue.o src/pmc/os.o src/pmc/file.o src/pmc/addrregistry.o src/pmc/bound_nci.o src/pmc/capture.o src/pmc/class.o src/pmc/codestring.o src/pmc/deleg_pmc.o src/pmc/enumerate.o src/pmc/eventhandler.o src/pmc/exceptionhandler.o src/pmc/exporter.o src/pmc/fixedbooleanarray.o src/pmc/fixedfloatarray.o src/pmc/fixedpmcarray.o src/pmc/lexinfo.o src/pmc/multisub.o src/pmc/namespace.o src/pmc/object.o src/pmc/pair.o src/pmc/parrotrunningthread.o src/pmc/pccmethod_test.o src/pmc/pmcproxy.o src/pmc/resizablebooleanarray.o src/pmc/resizablefloatarray.o src/pmc/resizableintegerarray.o src/pmc/resizablepmcarray.o src/pmc/resizablestringarray.o src/pmc/role.o src/pmc/scalar.o src/pmc/scheduler.o src/pmc/schedulermessage.o src/pmc/slice.o src/pmc/stmlog.o src/pmc/stmref.o src/pmc/stmvar.o src/pmc/task.o src/pmc/undef.o src/encodings/fixed_8.o src/encodings/ucs2.o src/encodings/utf16.o src/encodings/utf8.o compilers/imcc/imcparser.o compilers/imcc/imclexer.o compilers/imcc/imc.o compilers/imcc/main.o compilers/imcc/symreg.o compilers/imcc/instructions.o compilers/imcc/cfg.o compilers/imcc/reg_alloc.o compilers/imcc/sets.o compilers/imcc/debug.o compilers/imcc/optimizer.o compilers/imcc/pbc.o compilers/imcc/parser_util.o compilers/imcc/pcc.o src/packdump.o src/pbc_merge.o compilers/imcc/imcc.y MK_I has no POD mk_pmc_const has no POD func_ins has no POD clear_state has no POD INS_LABEL has no POD iLABEL has no POD iSUBROUTINE has no POD iINDEXFETCH has no POD iINDEXSET has no POD inv_op has no POD IMCC_create_itcall_label has no POD mk_sub_address_fromc has no POD mk_sub_address_u has no POD IMCC_itcall_sub has no POD begin_return_or_yield has no POD set_lexical has no POD add_pcc_named_arg has no POD add_pcc_named_result has no POD add_pcc_named_param has no POD add_pcc_named_return has no POD adv_named_set has no POD do_loadlib has no POD Parrot_debugger_start has no POD pass_exception_args has no POD couldn't read 'src/exec_cpu.c': No such file or directory at tools/build/headerizer.pl line 365. make: *** [headerizer] Error 2 So I never got to 'make' per se; the problem is in tools/build/headerizer.pl's action.