Update autoconf rules. Fixes bug url to point to github issues.

autogen.sh

@@ -3,6 +3,15 @@
 # Create configure and makefile stuff...
 #
 
+# Git hooks should come before autoreconf.
+if test -d .git; then
+  if ! test -d .git; then
+    mkdir .git/hooks
+  fi
+  ln -s -f ../../pre-commit.sh .git/hooks/pre-commit
+fi
+
+# If this is a source checkout then call autoreconf with error as well
 if test -d .git; then
   WARNINGS="all,error"
 else
@@ -11,6 +20,3 @@ fi
 
 autoreconf --install --force --verbose
 
-if test -d .git; then
-    ln -s -f ../../pre-commit.sh .git/hooks/pre-commit
-fi