http://bugs.gentoo.org/107435
http://lists.gnu.org/archive/html/automake/2005-09/msg00088.html

2005-09-27  Stepan Kasal  <address@hidden>

	* automake.in (handle_single_transform): Direct suffix rule preserves
	  the directory prefix, so the generated object name should contain
	  it, too.

--- a/automake.in	2005-09-17 15:05:39.000000000 +0200
+++ b/automake.in	2005-09-27 17:10:47.000000000 +0200
@@ -1755,6 +1755,10 @@
             # This is probably the result of a direct suffix rule.
             # In this case we just accept the rewrite.
             $object = "$base$extension";
+            if ($directory ne '')
+            {
+                $object = $directory . '/' . $object;
+            }
             $linker = '';
         }
         else
@@ -1824,7 +1828,7 @@
 
 		# For Java, the way we're handling it right now, a
 		# `..' component doesn't make sense.
-                if ($lang->name eq 'java' && $object =~ /(\/|^)\.\.\//)
+                if ($lang && $lang->name eq 'java' && $object =~ /(\/|^)\.\.\//)
 		  {
 		    err_am "`$full' should not contain a `..' component";
 		  }