Attached patch fixes the issue. It also moves the manpages into the -server package, since they are also used by the check_mk script on the CLI.

It's not a perfect solution since in theory one could use the -multisite webgui without the server, but I'm not sure whether this is in use anywhere. Alternatively the manpages could stay in check-mk-doc and just moved somewhere else.
diff -ur a/debian/check-mk-server.install b/debian/check-mk-server.install
--- a/debian/check-mk-server.install	2011-11-22 18:46:48.000000000 +0000
+++ b/debian/check-mk-server.install	2012-01-19 00:07:57.000000000 +0000
@@ -8,6 +8,7 @@
 var/lib/check_mk/precompiled
 usr/bin/check_mk
 usr/share/check_mk/checks
+usr/share/check_mk/checks-man
 usr/share/check_mk/modules
 usr/share/check_mk/pnp-rraconf
 usr/share/check_mk/pnp-templates
diff -ur a/debian/defaults.icinga b/debian/defaults.icinga
--- a/debian/defaults.icinga	2011-11-22 18:46:48.000000000 +0000
+++ b/debian/defaults.icinga	2012-01-19 00:06:08.000000000 +0000
@@ -11,7 +11,7 @@
 default_config_dir          = '/etc/check_mk'
 check_mk_configdir          = '/etc/check_mk/conf.d'
 checks_dir                  = '/usr/share/check_mk/checks'
-check_manpages_dir          = '/usr/share/doc/check_mk/checks'
+check_manpages_dir          = '/usr/share/check_mk/checks-man'
 modules_dir                 = '/usr/share/check_mk/modules'
 locale_dir                  = '/usr/share/check_mk/locale'
 agents_dir                  = '/usr/share/check_mk/agents'
diff -ur a/debian/defaults.nagios3 b/debian/defaults.nagios3
--- a/debian/defaults.nagios3	2011-11-22 18:46:48.000000000 +0000
+++ b/debian/defaults.nagios3	2012-01-19 00:06:23.000000000 +0000
@@ -11,7 +11,7 @@
 default_config_dir          = '/etc/check_mk'
 check_mk_configdir          = '/etc/check_mk/conf.d'
 checks_dir                  = '/usr/share/check_mk/checks'
-check_manpages_dir          = '/usr/share/doc/check_mk/checks'
+check_manpages_dir          = '/usr/share/check_mk/checks-man'
 modules_dir                 = '/usr/share/check_mk/modules'
 locale_dir                  = '/usr/share/check_mk/locale'
 agents_dir                  = '/usr/share/check_mk/agents'
diff -ur a/debian/rules b/debian/rules
--- a/debian/rules	2011-11-22 18:46:48.000000000 +0000
+++ b/debian/rules	2012-01-19 00:11:37.000000000 +0000
@@ -83,7 +83,8 @@
 	cp debian/tmp/usr/share/check_mk/agents/xinetd.conf debian/check-mk-agent/etc/xinetd.d/check_mk
 	# xinetd: Disable service
 	sed -i 's#disable\s*=\s*no#disable        = yes#' debian/check-mk-agent/etc/xinetd.d/check_mk
-
+	# move checks manpages (to be installed in -server)
+	mv debian/tmp/usr/share/doc/check_mk/checks debian/tmp/usr/share/check_mk/checks-man
 
 # Build architecture-independent files here.
 binary-indep: build install

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