The following files are all generated and shouldn't be distributed or in CVS:

   Makefile.global-vars
   config.log
   config.status

   contrib/apache/offline.conf

   src/common/etc/configure_etc.sh
   src/common/etc/database/DB.conf
   src/common/etc/openca_rc
   src/common/etc/openca_start.template
   src/common/etc/openca_stop.template
   src/common/etc/utf8_latin1_selector.sh.template

   src/common/var/crypto/Makefile.crt

   src/modules/openca-openssl/const-c.inc
   src/modules/openca-openssl/const-xs.inc

   src/scripts/openca-addreq

   src/web-interfaces/batch/access_control.xml
   src/web-interfaces/batch/batch.conf
   src/web-interfaces/ca/access_control.xml
   src/web-interfaces/ca/ca.conf
   src/web-interfaces/ldap/access_control.xml
   src/web-interfaces/ldap/ldap.conf
   src/web-interfaces/node/access_control.xml
   src/web-interfaces/node/node.conf
   src/web-interfaces/pub/access_control.xml
   src/web-interfaces/pub/public.conf
   src/web-interfaces/ra/access_control.xml
   src/web-interfaces/ra/ra.conf
   src/web-interfaces/scep/access_control.xml
   src/web-interfaces/scep/scep.conf

Most of these are present because they aren't being cleaned up in the distclean rule. The attached patch fixes the distclean rules to include the missing files and fix a couple of bugs. There are still a couple of remaining stragglers that didn't get fixed because they're Perl modules and I wasn't sure how to fix the Makefile.PL files.

It also eliminates a circular dependency between configure and Makefile.global-vars.

The openca_stop.template file wasn't being processed by configure, as a result, the variables weren't being expanded. The existing src/common/etc/openca_stop.template should be renamed to openca_stop.template.in.

The configure file needs to be regenerated by autoconf due to these changes to configure.in.

Index: configure.in
===================================================================
--- configure.in        (.../vendor/openca)     (revision 3)
+++ configure.in        (.../trunk/openca)      (revision 13)
@@ -469,8 +469,10 @@
                $PATH:/usr/ccs/bin)
 
        AC_MSG_CHECKING([$MAKE silent mode (-s)])
-       if $MAKE -s help 2>&1 >/dev/null; then
-               MAKE="$MAKE -s" ;
+       echo 'help:' > conftest.mak
+       echo '  ' >> conftest.mak
+       if $MAKE -s -f conftest.mak help >/dev/null 2>&1; then
+               MAKE="$MAKE -s"
                AC_MSG_RESULT( [ok])
        else
                AC_MSG_ERROR( [unsupported])
@@ -598,6 +600,7 @@
                src/common/etc/configure_etc.sh
                src/common/etc/log.xml
                src/common/etc/openca_start.template
+               src/common/etc/openca_stop.template
                src/common/etc/openca_rc
                src/common/etc/token.xml
                src/common/etc/loa.xml
Index: src/scripts/Makefile
===================================================================
--- src/scripts/Makefile        (.../vendor/openca)     (revision 3)
+++ src/scripts/Makefile        (.../trunk/openca)      (revision 13)
@@ -8,6 +8,7 @@
 # scripts derived from .in files:
 AC_SCRIPTS     = \
        openca-addcert          \
+       openca-addreq           \
        openca-backup           \
        openca-configure        \
        openca-dblist           \
Index: src/common/var/crypto/Makefile
===================================================================
--- src/common/var/crypto/Makefile      (.../vendor/openca)     (revision 3)
+++ src/common/var/crypto/Makefile      (.../trunk/openca)      (revision 13)
@@ -99,6 +99,8 @@
        $(MAKE) __install_dir USER=${httpd_user} GROUP=${httpd_group} MODE=750 
DIR=$(DEST_DIR)$(var_prefix)/$@
 
 distclean::
-
+       for i in $(MAKECHAIN); do \
+               if test -e $$i ; then rm $$i ; fi \
+       done
 #              $(RM) $(AC_CONFOPENSSLFILES)
 #              $(RM) $(AC_FILES)
Index: src/common/etc/openca_stop.template.in (Copied from 
openca_start.template)
===================================================================
--- src/common/etc/openca_stop.template.in      (.../vendor/openca)     
(revision 0)
+++ src/common/etc/openca_stop.template.in      (.../trunk/openca)      
(revision 13)
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+echo -n Stopping XML cache ...
+PID=`cat @var_prefix@/tmp/xml_cache.pid 2>/dev/null`;
+[ -n "$PID" ] && kill $PID
+echo done
+
+echo -n Stopping openca server ...
+PID=`cat @var_prefix@/tmp/openca_socket.pid 2>/dev/null`;
+[ -n "$PID" ] && kill $PID
+echo done

Index: src/common/etc/database/Makefile
===================================================================
--- src/common/etc/database/Makefile    (.../vendor/openca)     (revision 3)
+++ src/common/etc/database/Makefile    (.../trunk/openca)      (revision 13)
@@ -31,7 +31,7 @@
                $(INSTALL) -o ${openca_user} -g ${openca_group} -m 644 $@ 
$(DEST_CGI_CONFDIR)/[EMAIL PROTECTED]
 
 distclean::
-               for i in $(AC_CONFFILES) ; do \
+               for i in $(AC_FILES) ; do \
                        if test -e $$i ; then $(RM) "$$i" ; fi ;\
                done
 
Index: src/common/etc/Makefile
===================================================================
--- src/common/etc/Makefile     (.../vendor/openca)     (revision 3)
+++ src/common/etc/Makefile     (.../trunk/openca)      (revision 13)
@@ -44,7 +44,7 @@
        openca_start.template   \
        openca_stop.template    \
        openca_rc               \
-        utf8_latin1_selector.sh.template
+       utf8_latin1_selector.sh.template
 
 #---- variable settings above, rules below ----
 
@@ -84,7 +84,7 @@
                $(INSTALL) -o ${openca_user} -g ${openca_group} -m 755 $@ 
$(DEST_DIR)$(etc_prefix)/$@
 
 distclean::
-               for i in $(AC_FILES) ; do \
+               for i in $(AC_FILES) $(PROGS); do \
                        if test -e $$i ; then $(RM) "$$i" ; fi ;\
                done
 
Index: src/web-interfaces/ldap/Makefile
===================================================================
--- src/web-interfaces/ldap/Makefile    (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/ldap/Makefile    (.../trunk/openca)      (revision 13)
@@ -74,7 +74,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/batch/Makefile
===================================================================
--- src/web-interfaces/batch/Makefile   (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/batch/Makefile   (.../trunk/openca)      (revision 13)
@@ -74,7 +74,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/ra/Makefile
===================================================================
--- src/web-interfaces/ra/Makefile      (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/ra/Makefile      (.../trunk/openca)      (revision 13)
@@ -74,7 +74,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/ca/Makefile
===================================================================
--- src/web-interfaces/ca/Makefile      (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/ca/Makefile      (.../trunk/openca)      (revision 13)
@@ -74,7 +74,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/node/Makefile
===================================================================
--- src/web-interfaces/node/Makefile    (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/node/Makefile    (.../trunk/openca)      (revision 13)
@@ -79,7 +79,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/pub/Makefile
===================================================================
--- src/web-interfaces/pub/Makefile     (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/pub/Makefile     (.../trunk/openca)      (revision 13)
@@ -84,7 +84,7 @@
                cd $@ && $(MAKE) $(SUBTARGET)
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: src/web-interfaces/scep/Makefile
===================================================================
--- src/web-interfaces/scep/Makefile    (.../vendor/openca)     (revision 3)
+++ src/web-interfaces/scep/Makefile    (.../trunk/openca)      (revision 13)
@@ -72,7 +72,7 @@
                $(MAKE) __install_ln_s TARGET=$(DEST_CGIDIR)/$(PROGS) 
LINK=$(DEST_CGIDIR)/$@
 
 distclean::
-       for i in $(AC_PROGS) ; do \
+       for i in $(AC_PROGS) $(CONF_FILE) $(AC_CONF_SRC); do \
                if test -e $$i ; then rm $$i ; fi \
        done
 
Index: Makefile
===================================================================
--- Makefile    (.../vendor/openca)     (revision 3)
+++ Makefile    (.../trunk/openca)      (revision 13)
@@ -118,7 +118,7 @@
 distclean::
                @for i in config.status config.cache config.log \
                                        Makefile.global-vars ; do \
-                       if test -e $i ; then rm -rf $i ; fi; \
+                       if test -e $$i ; then rm -rf $$i ; fi; \
                done
 
                #$(RM) config.status config.cache config.log
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