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Hmmmmm. Now I'm confused. Is this what you meant?
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% hg diff
diff -r 019a2390b014 Makefile.pre.in
--- a/Makefile.pre.in Tue Aug 21 23:41:43 2012 +0000
+++ b/Makefile.pre.in Thu Aug 30 07:16:55 2012 +0000
@@ -43,6 +43,8 @@
 
 GNULD= @GNULD@
 
+MKDIR_P= @MKDIR_P@
+
 # Shell used by make (some versions default to the login shell, which is bad)
 SHELL= /bin/sh
 
@@ -223,8 +225,8 @@
 
 ##########################################################################
 # Grammar
-GRAMMAR_H= $(srcdir)/Include/graminit.h
-GRAMMAR_C= $(srcdir)/Python/graminit.c
+GRAMMAR_H= Include/graminit.h
+GRAMMAR_C= Python/graminit.c
 GRAMMAR_INPUT= $(srcdir)/Grammar/Grammar
 
 
@@ -266,9 +268,9 @@
 
 ##########################################################################
 # AST
-AST_H_DIR= $(srcdir)/Include
+AST_H_DIR= Include
 AST_H= $(AST_H_DIR)/Python-ast.h
-AST_C_DIR= $(srcdir)/Python
+AST_C_DIR= Python
 AST_C= $(AST_C_DIR)/Python-ast.c
 AST_ASDL= $(srcdir)/Parser/Python.asdl
 
@@ -605,9 +607,11 @@
 Parser/pgenmain.o: $(srcdir)/Include/parsetok.h
 
 $(AST_H): $(AST_ASDL) $(ASDLGEN_FILES)
+ $(MKDIR_P) $(AST_H_DIR)
 $(ASDLGEN) -h $(AST_H_DIR) $(AST_ASDL)
 
 $(AST_C): $(AST_ASDL) $(ASDLGEN_FILES)
+ $(MKDIR_P) $(AST_C_DIR)
 $(ASDLGEN) -c $(AST_C_DIR) $(AST_ASDL)
 
 Python/compile.o Python/symtable.o Python/ast.o: $(GRAMMAR_H) $(AST_H)
diff -r 019a2390b014 configure
--- a/configure Tue Aug 21 23:41:43 2012 +0000
+++ b/configure Thu Aug 30 07:16:55 2012 +0000
@@ -658,6 +658,7 @@
 GNULD
 LINKCC
 LDVERSION
+MKDIR_P
 RUNSHARED
 INSTSONAME
 LDLIBRARYDIR
@@ -5262,6 +5263,7 @@
 HGBRANCH=""
 fi
 
+MKDIR_P="mkdir -p"
 
 DISABLE_ASDLGEN=""
 # Extract the first word of "python", so it can be a program name with args.
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Given your "which actually isn't normally mkdir -p" comment... my patch doesn't seem right.