diff --git a/.gitignore b/.gitignore
index 837a72ef9f4d89d4679235902646bc34473ed0f6..5765184c961b4ff7c5b86a81dd6f7938b28b2d5b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -230,6 +230,24 @@ MAC/Test/TestHarness/THPVSSBridge/lofarconf
 MAC/Test/TestHarness/TSE/Makefile.common
 MAC/Test/TestHarness/TSE/autoconf_share
 MAC/Test/TestHarness/TSE/lofarconf
+RTCP/CNProc/Makefile.common
+RTCP/CNProc/autoconf_share
+RTCP/CNProc/lofarconf
+RTCP/IONProc/Makefile.common
+RTCP/IONProc/autoconf_share
+RTCP/IONProc/lofarconf
+RTCP/Interface/Makefile.common
+RTCP/Interface/autoconf_share
+RTCP/Interface/lofarconf
+RTCP/RTCPTools/Makefile.common
+RTCP/RTCPTools/autoconf_share
+RTCP/RTCPTools/lofarconf
+RTCP/Run/Makefile.common
+RTCP/Run/autoconf_share
+RTCP/Run/lofarconf
+RTCP/Storage/Makefile.common
+RTCP/Storage/autoconf_share
+RTCP/Storage/lofarconf
 SAS/OTB/MoM-OTDB-adapter/bin
 SAS/OTB/MoM-OTDB-adapter/dist/tasks
 SAS/OTB/MoM-OTDB-adapter/tasks
diff --git a/CEP/Imager/MWControl/configure.in b/CEP/Imager/MWControl/configure.in
index 7e0646a154a445cea41e405eb9760a7ddde7f6f7..1383218b1fe14949cfc89589a425edf416e26de8 100644
--- a/CEP/Imager/MWControl/configure.in
+++ b/CEP/Imager/MWControl/configure.in
@@ -52,7 +52,7 @@ dnl Check for LOFAR specific things
 dnl
 lofar_GENERAL
 lofar_INTERNAL(CEP/Imager/MWCommon,MWCommon,,1,MWCommon/MWConnection.h,,)
-lofar_INTERNAL(CEP/Calibration/BBSKernel,BBSKernel,,1,BBSKernel/Prediffer.h,,)
+lofar_INTERNAL(CEP/Calibration/BBSKernel,BBSKernel,,1,BBSKernel/Types.h,,)
 lofar_EXTERNAL(boost,1,boost/shared_ptr.hpp,"")
 
 dnl
diff --git a/MAC/APL/CEPCU/configure.in b/MAC/APL/CEPCU/configure.in
index 95fa78353df25e50187385e8aa8b56b05810cf94..270881158614858404721467e19a373078bb26a2 100644
--- a/MAC/APL/CEPCU/configure.in
+++ b/MAC/APL/CEPCU/configure.in
@@ -57,7 +57,7 @@ lofar_COMPILETOOLS
 lofar_PVSS(1)
 lofar_INTERNAL(LCS/Common, Common,, 1, Common/LofarTypes.h,,)
 lofar_INTERNAL(LCS/ACC/APS, APS,, 1, APS/ParameterSet.h,,)
-lofar_INTERNAL(Appl/ApplCommon, ApplCommon,, 1, ApplCommon/Observation.h,,)
+lofar_INTERNAL(LCS/ApplCommon, ApplCommon,, 1, ApplCommon/Observation.h,,)
 lofar_INTERNAL(LCS/ACC/ALC, ALC,, 1, ALC/ApplControl.h,,)
 lofar_INTERNAL(LCS/ACC/PLC, PLC,, 1, PLC/PCCmd.h,,)
 dnl lofar_INTERNAL(SAS/OTDB, OTDB, , 1, OTDB/OTDBconnection.h,,)
diff --git a/MAC/APL/MainCU/configure.in b/MAC/APL/MainCU/configure.in
index 6c9cbd85c3737d728775a9a9591777823cc58558..f59213ce5d814514222f1d859d31461c9f01001a 100644
--- a/MAC/APL/MainCU/configure.in
+++ b/MAC/APL/MainCU/configure.in
@@ -63,7 +63,7 @@ lofar_INTERNAL(MAC/GCF/TM, GCFTM, , 1, GCF/TM/GCF_Task.h,,)
 lofar_INTERNAL(MAC/GCF/RTDB, GCFRTDB, , 1, GCF/RTDB/RTDB_PropertySet.h,,)
 lofar_INTERNAL(MAC/APL/APLCommon, APLCommon, , 1, APL/APLCommon/APL_Defines.h,,)
 lofar_INTERNAL(MAC/APL/RTDBCommon, RTDBCommon, , 1, APL/RTDBCommon/RTDButilities.h,,)
-lofar_INTERNAL(Appl/ApplCommon, ApplCommon, , 1, ApplCommon/Observation.h,,)
+lofar_INTERNAL(LCS/ApplCommon, ApplCommon, , 1, ApplCommon/Observation.h,,)
 lofar_EXTERNAL(boost,1,boost/date_time/date.hpp, boost_date_time)
 lofar_EXTERNAL(pqxx,2.5.5,pqxx/pqxx, pqxx)
 lofar_EXTERNAL(pq,,libpq-fe.h, pq, /usr/local/pgsql)
diff --git a/MAC/APL/StationCU/configure.in b/MAC/APL/StationCU/configure.in
index 42f7c05727c656f2d8255b0e97bbcc36666c7429..ab8133c727af821b4b23d0617804b0f71b86d3bd 100644
--- a/MAC/APL/StationCU/configure.in
+++ b/MAC/APL/StationCU/configure.in
@@ -58,7 +58,7 @@ lofar_PVSS(1)
 lofar_BLITZ
 lofar_INTERNAL(LCS/Common, Common,, 1, Common/LofarTypes.h,,)
 lofar_INTERNAL(LCS/ACC/APS, APS,, 1, APS/ParameterSet.h,,)
-lofar_INTERNAL(Appl/ApplCommon, ApplCommon,, 1, ApplCommon/Observation.h,,)
+lofar_INTERNAL(LCS/ApplCommon, ApplCommon,, 1, ApplCommon/Observation.h,,)
 dnl lofar_INTERNAL(SAS/OTDB, OTDB,, 1, OTDB/OTDBconnection.h,,)
 lofar_INTERNAL(MAC/MACIO, MACIO, , 1, MACIO/MACServiceInfo.h,,)
 lofar_INTERNAL(MAC/GCF/TM, GCFTM,, 1, GCF/TM/GCF_Task.h,,)
diff --git a/RTCP/Run/bootstrap b/RTCP/Run/bootstrap
index be0aa5082f702905c4cb89db7d6df5b590303556..fd49f5826a5501fdb92c129384c66f2835f940ac 100755
--- a/RTCP/Run/bootstrap
+++ b/RTCP/Run/bootstrap
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-../autoconf_share/bootstrap ../autoconf_share
+../../autoconf_share/bootstrap ../../autoconf_share
diff --git a/RTCP/Run/src/Makefile.am b/RTCP/Run/src/Makefile.am
index 41dd95b32ca229eff0832b36627d9f52cbd0da7b..3f2ac45ef8f0733d0e09325028778890d4ed6c49 100644
--- a/RTCP/Run/src/Makefile.am
+++ b/RTCP/Run/src/Makefile.am
@@ -34,7 +34,7 @@ dist_python_SCRIPTS = 	\
 			LOFAR_Jobs.py \
 			CS1_RSPCtl.py \
 			CS1_Run.py \
-			CS1_Sections.py \
+			CS1_Sections.py
 
 scriptdir = $(bindir)
 dist_script_SCRIPTS = 
diff --git a/SAS/lofarconf.in b/SAS/lofarconf.in
new file mode 100644
index 0000000000000000000000000000000000000000..c79ce2f67848b8189cf0a0501faf5cba9db11fde
--- /dev/null
+++ b/SAS/lofarconf.in
@@ -0,0 +1 @@
+OTDB
diff --git a/SubSystems/Offline/lofarconf.in b/SubSystems/Offline/lofarconf.in
index 1b50bfcd0b114b15b0b8621a7e5d02e2b1656572..796b6b5fdd6bd10d0b6175dfeaf167a0b1713bb6 100644
--- a/SubSystems/Offline/lofarconf.in
+++ b/SubSystems/Offline/lofarconf.in
@@ -1,4 +1,4 @@
-/CEP/BB/BBSControl
-/CEP/BB/pyparmdb
-/CEP/BB/MWImager
-/Appl/CEP/CS1/CS1_pp_lib
+/CEP/Calibration/BBSControl
+/CEP/pyparmdb
+/CEP/Imager/MWImager
+/CEP/DP3/CS1_pp_lib
diff --git a/SubSystems/lofarconf.in b/SubSystems/lofarconf.in
new file mode 100644
index 0000000000000000000000000000000000000000..a78e6a314594267df8a26c58d276dcc16ffa5577
--- /dev/null
+++ b/SubSystems/lofarconf.in
@@ -0,0 +1,4 @@
+CEPCU_MAC
+LCU_MAC
+MCU_MAC
+Offline