With this patch you can rename user-commands/xindy.v2.in => user-commands/xindy.v2 and simplify user-commands/Makefile.am accordingly. diff -ur -x Makefile.in -x aclocal.m4 -x configure -x autom4te.cache xindy.orig/user-commands/texindy xindy/user-commands/texindy --- xindy.orig/user-commands/texindy 2009-03-22 12:09:29.000000000 +0100 +++ xindy/user-commands/texindy 2009-11-24 22:03:22.000000000 +0100 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#! /usr/bin/env perl # $Id: texindy,v 1.8 2009/03/22 11:08:18 jschrod Exp $ #------------------------------------------------------------ # (history at end) diff -ur -x Makefile.in -x aclocal.m4 -x configure -x autom4te.cache xindy.orig/user-commands/xindy.in xindy/user-commands/xindy.in --- xindy.orig/user-commands/xindy.in 2009-03-29 13:14:55.000000000 +0200 +++ xindy/user-commands/xindy.in 2009-11-24 22:03:21.000000000 +0100 @@ -1,4 +1,4 @@ -#!/usr/bin/perl +#! /usr/bin/env perl # $Id: xindy.pl,v 1.13 2009/03/29 11:14:04 jschrod Exp $ #------------------------------------------------------------ # (history at end) diff -ur -x Makefile.in -x aclocal.m4 -x configure -x autom4te.cache xindy.orig/user-commands/xindy.v2.in xindy/user-commands/xindy.v2.in --- xindy.orig/user-commands/xindy.v2.in 2005-05-30 23:10:02.000000000 +0200 +++ xindy/user-commands/xindy.v2.in 2009-11-24 22:03:35.000000000 +0100 @@ -1,4 +1,4 @@ -#!@XINDY_PERL@ +#! /usr/bin/env perl # $Id: xindy.in,v 1.14 2005/05/02 19:16:27 jschrod Exp $ #------------------------------------------------------------ #