diff --git a/appvm/qubes.rules b/appvm/qubes.rules
index e3fc50e4..5b3a502b 100644
--- a/appvm/qubes.rules
+++ b/appvm/qubes.rules
@@ -1 +1 @@
-SUBSYSTEM=="block", KERNEL=="xvdh", ACTION=="add", RUN+="/usr/bin/qubes_add_pendrive_script"
+SUBSYSTEM=="block", KERNEL=="xvdh", ACTION=="add", RUN+="/usr/lib/qubes/qubes_add_pendrive_script"
diff --git a/appvm/qubes_add_pendrive_script.c b/appvm/qubes_add_pendrive_script.c
index 41823aeb..bb708610 100644
--- a/appvm/qubes_add_pendrive_script.c
+++ b/appvm/qubes_add_pendrive_script.c
@@ -189,7 +189,7 @@ void dvm_transaction_request(char *seq, struct xs_handle *xs)
 	if (stat_pre.st_mtime == stat_post.st_mtime)
 		suicide(xs);
 	xs_daemon_close(xs);
-	execl("/usr/bin/qvm-dvm-transfer", "qvm-dvm-transfer", src_vm,
+	execl("/usr/lib/qubes/qvm-dvm-transfer", "qvm-dvm-transfer", src_vm,
 	      filename, seq, NULL);
 	syslog(LOG_DAEMON | LOG_ERR, "execl qvm-dvm-transfer");
 	suicide(xs);
diff --git a/appvm/qvm-copy-to-vm b/appvm/qvm-copy-to-vm
index def32d7c..1af03ec0 100755
--- a/appvm/qvm-copy-to-vm
+++ b/appvm/qvm-copy-to-vm
@@ -24,7 +24,7 @@ if [ $# -lt 2 ] ; then
 	echo usage: $0 'vmname file [file]*'
 	exit 1
 fi
-qubes_penctl new || exit 1
+/usr/lib/qubes/qubes_penctl new || exit 1
 echo -n Waiting for the Qubes virtual pendrive
 while ! [ -e /dev/xvdg ] ; do
 	echo -n .
@@ -37,4 +37,4 @@ shift
 cp -v -a "$@" /mnt/outgoing
 #sometimes Dolphin lags a bit
 umount /mnt/outgoing || (sleep 1; umount /mnt/outgoing) || exit 1
-qubes_penctl send $VMNAME || exit 1
+/usr/lib/qubes/qubes_penctl send $VMNAME || exit 1
diff --git a/appvm/qvm-copy.desktop b/appvm/qvm-copy.desktop
index 6d7ebc66..5795eb61 100644
--- a/appvm/qvm-copy.desktop
+++ b/appvm/qvm-copy.desktop
@@ -4,7 +4,7 @@ Type=Service
 X-KDE-ServiceTypes=KonqPopupMenu/Plugin,inode/directory,all/allfiles
 
 [Desktop Action QvmCopy]
-Exec=/usr/bin/qvm-copy-to-vm.kde %U
+Exec=/usr/lib/qubes/qvm-copy-to-vm.kde %U
 Icon=kget
 Name=Send To VM
 
diff --git a/common/qubes_nmhook b/common/qubes_nmhook
index d06cd57d..b9028de8 100755
--- a/common/qubes_nmhook
+++ b/common/qubes_nmhook
@@ -1,2 +1,2 @@
 #!/bin/sh
-/usr/bin/qubes_setup_dnat_to_ns
+/usr/lib/qubes/qubes_setup_dnat_to_ns
diff --git a/common/qubes_setup_dnat_to_ns b/common/qubes_setup_dnat_to_ns
index e4841919..67a1b90b 100755
--- a/common/qubes_setup_dnat_to_ns
+++ b/common/qubes_setup_dnat_to_ns
@@ -10,7 +10,7 @@ addrule()
         fi
 }
 export PATH=$PATH:/sbin:/bin
-source /var/run/qubes_ns
+source /var/run/qubes/qubes_ns
 if [ "X"$NS1 = "X" ] ; then exit ; fi
 iptables -t nat -F PREROUTING
 FIRSTONE=yes
diff --git a/dom0/init.d/qubes_netvm b/dom0/init.d/qubes_netvm
index 45ae08fa..5e66b695 100755
--- a/dom0/init.d/qubes_netvm
+++ b/dom0/init.d/qubes_netvm
@@ -35,9 +35,9 @@ start()
         brctl setfd br0 1
         ifconfig br0 10.0.0.1 netmask 255.255.0.0 up || exit 1
         ifconfig br0:1 10.0.255.254 netmask 255.255.0.0 up || exit 1
-        echo "NS1=10.0.0.1" > /var/run/qubes_ns
-        echo "NS2=10.0.255.254" >> /var/run/qubes_ns
-        qubes_setup_dnat_to_ns
+        echo "NS1=10.0.0.1" > /var/run/qubes/qubes_ns
+        echo "NS2=10.0.255.254" >> /var/run/qubes/qubes_ns
+        /usr/lib/qubes/qubes_setup_dnat_to_ns
         echo "1" > /proc/sys/net/ipv4/ip_forward || exit 1
     else
 
diff --git a/dom0/pendrive_swapper/qfilexchgd b/dom0/pendrive_swapper/qfilexchgd
index 9068cf10..be7f4650 100755
--- a/dom0/pendrive_swapper/qfilexchgd
+++ b/dom0/pendrive_swapper/qfilexchgd
@@ -196,7 +196,7 @@ class DomainState:
             logproc( 'Domain ' + vmname + ' does not exist ?')
             qvm_collection.unlock_db()
             return False
-        retcode = subprocess.call(['/usr/bin/qubes_restore',
+        retcode = subprocess.call(['/usr/lib/qubes/qubes_restore',
             current_savefile,
             '-c', vm.label.color,
             '-i', vm.label.icon,
diff --git a/dom0/restore/qubes_restore.c b/dom0/restore/qubes_restore.c
index 21bf8606..9ab3550e 100644
--- a/dom0/restore/qubes_restore.c
+++ b/dom0/restore/qubes_restore.c
@@ -371,7 +371,7 @@ void write_varrun_domid(int domid, char * dispname, char *orig)
 void redirect_stderr()
 {
 	int fd =
-	    open("/var/run/qubes/qubes_restore.log",
+	    open("/var/log/qubes/qubes_restore.log",
 		 O_CREAT | O_TRUNC | O_WRONLY, 0600);
 	if (fd < 0) {
 		syslog(LOG_DAEMON | LOG_ERR, "open qubes_restore.log");
diff --git a/netvm/qubes_core b/netvm/qubes_core
index 4be4f4c4..aebf4d7c 100755
--- a/netvm/qubes_core
+++ b/netvm/qubes_core
@@ -28,9 +28,9 @@ start()
     secondary_dns=$(/usr/bin/xenstore-read qubes_netvm_secondary_dns)
     ifconfig br0 $gateway netmask $netmask up
     ifconfig br0:1 $secondary_dns netmask $netmask
-    echo "NS1=$gateway" > /var/run/qubes_ns
-    echo "NS2=$secondary_dns" >> /var/run/qubes_ns
-    qubes_setup_dnat_to_ns
+    echo "NS1=$gateway" > /var/run/qubes/qubes_ns
+    echo "NS2=$secondary_dns" >> /var/run/qubes/qubes_ns
+    /usr/lib/qubes/qubes_setup_dnat_to_ns
     echo "1" > /proc/sys/net/ipv4/ip_forward
 #now no need for dnsmasq
 #    dnsmasq --listen-address $gateway --bind-interfaces
diff --git a/rpm_spec/core-appvm.spec b/rpm_spec/core-appvm.spec
index 143aa3dc..a4444f0b 100644
--- a/rpm_spec/core-appvm.spec
+++ b/rpm_spec/core-appvm.spec
@@ -61,10 +61,10 @@ mkdir -p $RPM_BUILD_ROOT/etc/init.d
 cp qubes_core $RPM_BUILD_ROOT/etc/init.d/
 mkdir -p $RPM_BUILD_ROOT/var/lib/qubes
 mkdir -p $RPM_BUILD_ROOT/usr/bin
-cp qubes_timestamp qubes_add_pendrive_script qubes_penctl \
-	qvm-copy-to-vm qvm-copy-to-vm.kde \
-	qvm-open-in-dvm $RPM_BUILD_ROOT/usr/bin
-ln -s qvm-open-in-dvm $RPM_BUILD_ROOT/usr/bin/qvm-dvm-transfer 
+cp qubes_timestamp qvm-copy-to-vm qvm-open-in-dvm $RPM_BUILD_ROOT/usr/bin
+mkdir -p $RPM_BUILD_ROOT/usr/lib/qubes
+cp qubes_add_pendrive_script qubes_penctl qvm-copy-to-vm.kde $RPM_BUILD_ROOT/usr/lib/qubes
+ln -s /usr/bin/qvm-open-in-dvm $RPM_BUILD_ROOT/usr/lib/qubes/qvm-dvm-transfer 
 mkdir -p $RPM_BUILD_ROOT/%{kde_service_dir}
 cp qvm-copy.desktop qvm-dvm.desktop $RPM_BUILD_ROOT/%{kde_service_dir}
 mkdir -p $RPM_BUILD_ROOT/etc/udev/rules.d
@@ -184,13 +184,13 @@ rm -rf $RPM_BUILD_ROOT
 /etc/fstab
 /etc/init.d/qubes_core
 /usr/bin/qvm-copy-to-vm
-/usr/bin/qvm-copy-to-vm.kde
+/usr/lib/qubes/qvm-copy-to-vm.kde
 %attr(4755,root,root) /usr/bin/qvm-open-in-dvm
-/usr/bin/qvm-dvm-transfer
+/usr/lib/qubes/qvm-dvm-transfer
 %{kde_service_dir}/qvm-copy.desktop
 %{kde_service_dir}/qvm-dvm.desktop
-%attr(4755,root,root) /usr/bin/qubes_penctl
-/usr/bin/qubes_add_pendrive_script
+%attr(4755,root,root) /usr/lib/qubes/qubes_penctl
+/usr/lib/qubes/qubes_add_pendrive_script
 /etc/udev/rules.d/qubes.rules
 /etc/sysconfig/iptables
 /var/lib/qubes
diff --git a/rpm_spec/core-dom0.spec b/rpm_spec/core-dom0.spec
index cdfd5e67..8d0068ad 100644
--- a/rpm_spec/core-dom0.spec
+++ b/rpm_spec/core-dom0.spec
@@ -58,9 +58,6 @@ mkdir -p $RPM_BUILD_ROOT/usr/bin/
 cp qvm-tools/qvm-* $RPM_BUILD_ROOT/usr/bin
 cp clipboard_notifier/qclipd $RPM_BUILD_ROOT/usr/bin
 cp pendrive_swapper/qfilexchgd $RPM_BUILD_ROOT/usr/bin
-cp restore/xenstore-watch $RPM_BUILD_ROOT/usr/bin
-cp restore/qubes_restore  $RPM_BUILD_ROOT/usr/bin
-cp restore/qubes_prepare_saved_domain.sh  $RPM_BUILD_ROOT/usr/bin
 
 mkdir -p $RPM_BUILD_ROOT/etc/xen/scripts
 cp restore/block.qubes $RPM_BUILD_ROOT/etc/xen/scripts
@@ -81,6 +78,10 @@ cp aux-tools/create_apps_for_appvm.sh $RPM_BUILD_ROOT/usr/lib/qubes
 cp aux-tools/remove_appvm_appmenus.sh $RPM_BUILD_ROOT/usr/lib/qubes
 cp pendrive_swapper/qubes_pencmd $RPM_BUILD_ROOT/usr/lib/qubes
 
+cp restore/xenstore-watch $RPM_BUILD_ROOT/usr/bin
+cp restore/qubes_restore  $RPM_BUILD_ROOT/usr/lib/qubes
+cp restore/qubes_prepare_saved_domain.sh  $RPM_BUILD_ROOT/usr/lib/qubes
+
 mkdir -p $RPM_BUILD_ROOT/var/lib/qubes
 mkdir -p $RPM_BUILD_ROOT/var/lib/qubes/vm-templates
 mkdir -p $RPM_BUILD_ROOT/var/lib/qubes/appvms
@@ -95,9 +96,9 @@ mkdir -p $RPM_BUILD_ROOT/etc/yum.repos.d
 cp ../dom0/qubes.repo $RPM_BUILD_ROOT/etc/yum.repos.d
 
 mkdir -p $RPM_BUILD_ROOT/usr/bin
-cp ../common/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/usr/bin
+cp ../common/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/usr/lib/qubes
 mkdir -p $RPM_BUILD_ROOT/etc/dhclient.d
-ln -s /usr/bin/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/etc/dhclient.d/qubes_setup_dnat_to_ns.sh 
+ln -s /usr/lib/qubes/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/etc/dhclient.d/qubes_setup_dnat_to_ns.sh 
 mkdir -p $RPM_BUILD_ROOT/etc/NetworkManager/dispatcher.d/
 cp ../common/qubes_nmhook $RPM_BUILD_ROOT/etc/NetworkManager/dispatcher.d/
 mkdir -p $RPM_BUILD_ROOT/etc/sysconfig
@@ -209,13 +210,13 @@ fi
 %attr(770,root,qubes) %dir /var/lib/qubes/dvmdata
 %dir /usr/share/qubes/icons/*.png
 /etc/yum.repos.d/qubes.repo
-/usr/bin/qubes_setup_dnat_to_ns
+/usr/lib/qubes/qubes_setup_dnat_to_ns
 /etc/dhclient.d/qubes_setup_dnat_to_ns.sh
 /etc/NetworkManager/dispatcher.d/qubes_nmhook
 /etc/sysconfig/iptables
 /usr/lib64/pm-utils/sleep.d/01qubes-sync-vms-clock
 /usr/lib64/pm-utils/sleep.d/02qubes-pause-vms
 /usr/bin/xenstore-watch
-/usr/bin/qubes_restore
-/usr/bin/qubes_prepare_saved_domain.sh
+/usr/lib/qubes/qubes_restore
+/usr/lib/qubes/qubes_prepare_saved_domain.sh
 /etc/xen/scripts/block.qubes
diff --git a/rpm_spec/core-netvm.spec b/rpm_spec/core-netvm.spec
index 4081dbb6..5d130e1b 100644
--- a/rpm_spec/core-netvm.spec
+++ b/rpm_spec/core-netvm.spec
@@ -59,10 +59,10 @@ cp fstab $RPM_BUILD_ROOT/etc/fstab
 mkdir -p $RPM_BUILD_ROOT/etc/init.d
 cp qubes_core $RPM_BUILD_ROOT/etc/init.d/
 mkdir -p $RPM_BUILD_ROOT/var/lib/qubes
-mkdir -p $RPM_BUILD_ROOT/usr/bin
-cp ../common/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/usr/bin
+mkdir -p $RPM_BUILD_ROOT/usr/lib/qubes
+cp ../common/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/usr/lib/qubes
 mkdir -p $RPM_BUILD_ROOT/etc/dhclient.d
-ln -s /usr/bin/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/etc/dhclient.d/qubes_setup_dnat_to_ns.sh 
+ln -s /usr/lib/qubes/qubes_setup_dnat_to_ns $RPM_BUILD_ROOT/etc/dhclient.d/qubes_setup_dnat_to_ns.sh 
 mkdir -p $RPM_BUILD_ROOT/etc/NetworkManager/dispatcher.d/
 cp ../common/qubes_nmhook $RPM_BUILD_ROOT/etc/NetworkManager/dispatcher.d/
 mkdir -p $RPM_BUILD_ROOT/etc/yum.repos.d
@@ -71,6 +71,7 @@ mkdir -p $RPM_BUILD_ROOT/sbin
 cp ../common/qubes_serial_login $RPM_BUILD_ROOT/sbin
 mkdir -p $RPM_BUILD_ROOT/etc
 cp ../common/serial.conf $RPM_BUILD_ROOT/var/lib/qubes/
+mkdir -p $RPM_BUILD_ROOT/var/run/qubes
 
 %triggerin -- initscripts
 cp /var/lib/qubes/serial.conf /etc/init/serial.conf
@@ -168,8 +169,9 @@ rm -rf $RPM_BUILD_ROOT
 /etc/sysconfig/iptables
 /etc/init.d/qubes_core
 /var/lib/qubes
-/usr/bin/qubes_setup_dnat_to_ns
+/usr/lib/qubes/qubes_setup_dnat_to_ns
 /etc/dhclient.d/qubes_setup_dnat_to_ns.sh
 /etc/NetworkManager/dispatcher.d/qubes_nmhook
 /etc/yum.repos.d/qubes.repo
 /sbin/qubes_serial_login
+%dir /var/run/qubes