diff --git a/README.md b/README.md
index d725c948a03811f839528ec3976cb828b75d1ea4..54db8cd5e4d2385fc9b2004c87e9fbbe0cf3f133 100644
--- a/README.md
+++ b/README.md
@@ -67,7 +67,7 @@ In addition *R* (https://www.r-project.org/) is required for pre- and
 postprocessing and run management (needs to be added to the PATH variable
 as well).
 
-For R some packages are required to run REMIND. All except of one (`gdxrrw`) are
+Some R packages are required to run REMIND. All except of one (`gdxrrw`) are
 either distributed via the offical R CRAN or via a separate repository hosted at
 PIK (PIK-CRAN). Before proceeding PIK-CRAN should be added to the list of
 available repositories via:
@@ -114,20 +114,20 @@ Make sure that the config file has been set correctly before
 starting the model.
 
 ## HOW TO CONTRIBUTE
-We are interested in working with you! Just contact us through GitHub
-(https://github.com/remindmodel) or by mail (remind@pik-potsdam.de) if you have
+We are interested in working with you! Contact us through GitHub
+(https://github.com/remindmodel) or by E-mail (remind@pik-potsdam.de) if you have
 found and/or fixed a bug, developed a new model feature, have ideas for further
-model development, suggestions for improvements or anything else. We are open to
+model development or suggestions for improvements. We are open to
 any kind of contribution. Our aim is to develop an open, transparent and
-meaningful energy-economy-model to get a better
-understanding of the underlying processes and possible futures. Join us doing
+meaningful energy-economy-model, and to get a better
+understanding of the underlying processes and possible futures. Join us in doing
 so!
 
 ## DEPENDENCIES
 Model dependencies **must be publicly available** and should be Open Source.
 Development aim is to rather minimize than expand dependencies on non-free
 and/or non open source software. That means that besides currently existing
-dependencies on GAMS, the GDXRRW R package and the corresponding solvers there
+dependencies on GAMS, the `gdxrrw` R package and the corresponding solvers there
 should be no additional dependencies of this kind and that these existing
 dependencies should be resolved in the future if possible.
 
diff --git a/config/default.cfg b/config/default.cfg
index c19cb72ea74768babca37723328ea9b469fb8320..f5fc570c23381d364efdc1173907891027993698 100755
--- a/config/default.cfg
+++ b/config/default.cfg
@@ -377,7 +377,7 @@ cfg$gms$cm_APscen              <- "SSP2"  # def <- SSP2
 cfg$gms$cm_Full_Integration    <- "off"   # def = off
 
 cfg$gms$c_CO2priceDependent_AdjCosts    <- "on"   # def = on
-cfg$gms$c_scaleEmiHistorical   <- "off"    # def = off
+cfg$gms$c_scaleEmiHistorical   <- "on"    # def = on
 
 # MAGICC configuration (AJS)
 # Calibrate year 2000 temperature to HADCRUT4 data (which is very close to AR5).
diff --git a/config/input.gdx b/config/input.gdx
index 35cae3b04c464265a1524103d6d1e3ed58e563e4..93c41b8f9af51dd42bfe1ba1f4dfe29f69dad341 100644
Binary files a/config/input.gdx and b/config/input.gdx differ
diff --git a/core/declarations.gms b/core/declarations.gms
index e560f50a82809d57741b8dc61bb4a6d4bf6bd3e3..95f9e994039c116708026c6ae0b7df101b23ca1c 100644
--- a/core/declarations.gms
+++ b/core/declarations.gms
@@ -261,9 +261,7 @@ vm_emiFgas(tall,all_regi,all_enty)                   "F-gas emissions by single
 positive variables
 ***----------------------------------------------------------------------------------------
 ***-------------------------------------------------MACRO module---------------------------
-vm_effGr(ttot,all_regi,all_in)                       "growth of factor efficiency"
 vm_enerSerAdj(tall,all_regi,all_in)                  "adjustment costs for energy service transformations"
-vm_damageFactor(ttot,all_regi)                       "damage factor reducing GDP"
 vm_esCapInv(ttot,all_regi,all_teEs)                   "investment for energy end-use capital at the energy service level"
 ***----------------------------------------------------------------------------------------
 *-----------------------------------------------ESM module---------------------------------
diff --git a/core/equations.gms b/core/equations.gms
index 310c89bd965601911427b71734538226be8e636a..a9647754c0bffa6573ca78bb749d4db0c48b69bc 100644
--- a/core/equations.gms
+++ b/core/equations.gms
@@ -467,12 +467,13 @@ q_costTeCapital(t,regi,teLearn) ..
 ***---------------------------------------------------------------------------
 *** this is to prevent that in the long term, all solids are supplied by biomass. Residential solids can be fully supplied by biomass (-> wood pellets), so the FE residential demand is subtracted
 *** vm_cesIO(t,regi,"fesob") will be 0 in the stationary realization
-q_limitBiotrmod(t,regi)$(t.val > 2050).. 
+q_limitBiotrmod(t,regi)$(t.val > 2020).. 
     vm_prodSe(t,regi,"pebiolc","sesobio","biotrmod") 
    - sum (in$sameAs("fesob",in), vm_cesIO(t,regi,in)) 
    - sum (fe2es(entyFe,esty,teEs)$buildMoBio(esty), vm_demFeForEs(t,regi,entyFe,esty,teEs) )
     =l=
-    3 * vm_prodSe(t,regi,"pecoal","sesofos","coaltr") 
+    (2 +  max(0,min(1,( 2100 - pm_ttot_val(t)) / ( 2100 - 2020 ))) * 3) !! 5 in 2020 and 2 in 2100
+    * vm_prodSe(t,regi,"pecoal","sesofos","coaltr") 
 ;
 
 ***-----------------------------------------------------------------------------
diff --git a/main.gms b/main.gms
index da45295c348290ee7bb5ec953140fcb3b1a5384e..c125509a3903ded2f27493d8625b3d9c5e323c5b 100644
--- a/main.gms
+++ b/main.gms
@@ -328,8 +328,8 @@ cm_fetaxscen        = 3;         !! def = 3
 cm_multigasscen     = 2;         !! def = 2
 cm_permittradescen  = 1;         !! def = 1
 cm_limit_peur_scen  = 1;         !! def = 1
-$setGlobal cm_oil_scen  medOil         !! def = medOil
-$setGlobal cm_gas_scen  medGas         !! def = medGas
+$setGlobal cm_oil_scen   medOil         !! def = medOil
+$setGlobal cm_gas_scen   medGas         !! def = medGas
 $setGlobal cm_coal_scen  medCoal        !! def = medCoal
 cm_rentdiscoil      = 0.2;       !! def 0.2
 cm_rentdiscoil2     = 0.9;       !! def 0.9
@@ -344,7 +344,7 @@ cm_earlyreti_rate   = 0.09;      !! def 0.09
 
 cm_so2tax_scen        = 1;         !! def =
 c_cint_scen           = 1;         !! def = 1
-cm_damage              = 0.005;     !! def = 0.005
+cm_damage             = 0.005;     !! def = 0.005
 cm_solwindenergyscen  = 1;         !! def = 1
 c_techAssumptScen     = 1;         !! def = 1
 c_ccsinjecratescen    = 1;         !! def = 1
@@ -368,7 +368,7 @@ cm_taxCO2inc_after_peakBudgYr = 2;      !! def = 2
 cm_CO2priceRegConvEndYr       = 2050;   !! def = 2050
 
 cm_trdadj            = 2;    !! def = 2.0
-cm_trdcst             = 1.5;  !! def = 1.5
+cm_trdcst            = 1.5;  !! def = 1.5
 c_refcapbnd          = 0;    !! def = 0
 cm_frac_CCS          = 10;   !! def = 10
 cm_frac_NetNegEmi    = 0.5;  !! def = 0.5
@@ -379,10 +379,10 @@ cm_damages_SccHorizon                 = 100;   !! def = 100
 cm_carbonprice_temperatureLimit       = 1.8;   !! def = 1.8
 
 
-cm_DiscRateScen = 0;!! def = 0
-cm_noReboundEffect = 0;
-$setGlobal cm_EsubGrowth  low  !! def = low
-$setGlobal c_scaleEmiHistorical  off  !! def = off
+cm_DiscRateScen        = 0;!! def = 0
+cm_noReboundEffect     = 0;
+$setGlobal cm_EsubGrowth         low  !! def = low
+$setGlobal c_scaleEmiHistorical  on  !! def = on
 
 
 $setGlobal c_regi_nucscen  all !! def = all
@@ -393,15 +393,15 @@ $setGlobal c_regi_capturescen  all !! def = all
 *** --------------------------------------------------------------------------------------------------------------------------------------------------------------------
 *--------------------flags------------------------------------------------------------
 $SETGLOBAL cm_SlowConvergence  off        !! def = off
-$setGlobal cm_nash_mode  debug   !! def = parallel
-$setGlobal c_EARLYRETIRE        on         !! def = on
-$setGlobal cm_OILRETIRE  off        !! def = off
-$setglobal cm_INCONV_PENALTY  on         !! def = on
-$setGlobal cm_so2_out_of_opt  on         !! def = on
-$setGlobal c_skip_output  off        !! def = off
-$setGlobal cm_MOFEX  off        !! def = off
-$setGlobal cm_conoptv  conopt3    !! def = conopt3
-$setGlobal cm_ccsfosall  off        !! def = off
+$setGlobal cm_nash_mode        debug      !! def = parallel
+$setGlobal c_EARLYRETIRE       on         !! def = on
+$setGlobal cm_OILRETIRE        off        !! def = off
+$setglobal cm_INCONV_PENALTY   on         !! def = on
+$setGlobal cm_so2_out_of_opt   on         !! def = on
+$setGlobal c_skip_output       off        !! def = off
+$setGlobal cm_MOFEX            off        !! def = off
+$setGlobal cm_conoptv          conopt3    !! def = conopt3
+$setGlobal cm_ccsfosall        off        !! def = off
 
 $setGlobal cm_APscen  SSP2          !! def = SSP2
 $setGlobal cm_magicc_calibrateTemperature2000  uncalibrated  !! def=uncalibrated
diff --git a/modules/20_growth/exogenous/declarations.gms b/modules/20_growth/exogenous/declarations.gms
new file mode 100644
index 0000000000000000000000000000000000000000..ef1c82f9ba6a80be290a38e3548755f2e864e88d
--- /dev/null
+++ b/modules/20_growth/exogenous/declarations.gms
@@ -0,0 +1,11 @@
+*** |  (C) 2006-2019 Potsdam Institute for Climate Impact Research (PIK)
+*** |  authors, and contributors see CITATION.cff file. This file is part
+*** |  of REMIND and licensed under AGPL-3.0-or-later. Under Section 7 of
+*** |  AGPL-3.0, you are granted additional permissions described in the
+*** |  REMIND License Exception, version 1.0 (see LICENSE file).
+*** |  Contact: remind@pik-potsdam.de
+*** SOF ./modules/20_growth/exogenous/declarations.gms
+positive variables
+vm_effGr(ttot,all_regi,all_in)            "growth of factor efficiency"
+;
+*** EOF ./modules/20_growth/exogenous/declarations.gms
diff --git a/modules/20_growth/exogenous/realization.gms b/modules/20_growth/exogenous/realization.gms
index 026e242d0b41ea4b0e22e127a179eb31019fc764..6afbb3dffe95d18476a3ac597d19b39044930002 100644
--- a/modules/20_growth/exogenous/realization.gms
+++ b/modules/20_growth/exogenous/realization.gms
@@ -16,6 +16,7 @@
 *' growth paths in reaction of policy shocks. This correction is done by an adjustment of capital accumulation.
 
 *####################### R SECTION START (PHASES) ##############################
+$Ifi "%phase%" == "declarations" $include "./modules/20_growth/exogenous/declarations.gms"
 $Ifi "%phase%" == "bounds" $include "./modules/20_growth/exogenous/bounds.gms"
 *######################## R SECTION END (PHASES) ###############################
 *** EOF ./modules/20_growth/exogenous.gms
diff --git a/modules/20_growth/spillover/declarations.gms b/modules/20_growth/spillover/declarations.gms
index d861ca228be5700d05f46f1b5489661f84173560..6333cbadddc64714a75768dc129a87968c25408e 100644
--- a/modules/20_growth/spillover/declarations.gms
+++ b/modules/20_growth/spillover/declarations.gms
@@ -24,6 +24,7 @@ Parameters
 
 *mlb*  vm_invInno and  vm_invImi and pm_cumEff shifted to the core folder
 Positive variables
+ vm_effGr(ttot,all_regi,all_in)            "growth of factor efficiency"
  v20_effInno(ttot,all_regi,all_in)         "efficiency improvement by innovation"
  v20_effImi(ttot,all_regi,all_in)          "efficiency improvement by imitation"
 ;
diff --git a/modules/32_power/IntC/realization.gms b/modules/32_power/IntC/realization.gms
index 268ee0445d0d02a64a36624f42ce551e79f29acd..9acb0a5a87a9e1480f6f767a9e1f5d85d9e274a6 100644
--- a/modules/32_power/IntC/realization.gms
+++ b/modules/32_power/IntC/realization.gms
@@ -8,17 +8,17 @@
 
 *' @description  
 *'
-*'The `IntC` realization (Integrated Costs) assume a single electricity market balance.
+*'The `IntC` realization (Integrated Costs) assumes a single electricity market balance.
 *'
-*'This module determine power system supply specific technology behavior, which summs up to the general core capacity equations to define the power sector operation and investment decisions.
+*'This module determines power system supply specific technology behavior, which sums up to the general core capacity equations to define the power sector operation and investment decisions.
 *'
-*'Contrary to other secondary energies in REMIND, this requires to move the electricity secondary energy balance (supply = demand) from the core to the module code.
+*'Contrary to other secondary energy types in REMIND, this requires to move the electricity secondary energy balance (supply = demand) from the core to the module code.
 *'
 *'
 *'In summary, the specific power technology equations found in this module reflect the points below.
 *'
 *'
-*'Storage requirements are based on intermittent renewables share, sinergies between different renewables production profiles and curtailment.
+*'Storage requirements are based on intermittent renewables share, synergies between different renewables production profiles and curtailment.
 *'
 *'Additional grid capacities are calculated for high intermittent renewable capacity (solar and wind) and regional spatial differences. 
 *'
diff --git a/modules/50_damages/BurkeLike/declarations.gms b/modules/50_damages/BurkeLike/declarations.gms
index 2091c966591ca726878654e0341aa6d28f3ea6f5..8d886c33e816d59ce709b3853c31fcfd4d72c8c3 100644
--- a/modules/50_damages/BurkeLike/declarations.gms
+++ b/modules/50_damages/BurkeLike/declarations.gms
@@ -4,8 +4,13 @@
 *** |  AGPL-3.0, you are granted additional permissions described in the
 *** |  REMIND License Exception, version 1.0 (see LICENSE file).
 *** |  Contact: remind@pik-potsdam.de
-
+*** SOF ./modules/50_damages/BurkeLike/declarations.gms
 parameters
 p50_damageFuncCoef1     "coef1 of damamge function",
 p50_damageFuncCoef2     "coef2 of damamge function"
 ;
+
+positive variable
+vm_damageFactor(ttot,all_regi)      "damage factor reducing GDP"
+;
+*** EOF ./modules/50_damages/BurkeLike/declarations.gms
diff --git a/modules/50_damages/DiceLike/declarations.gms b/modules/50_damages/DiceLike/declarations.gms
index a3e8cc1f0dc90ec1efb1a1029b8966804b99ffb1..d03b467b44a81ef0daa5cb34da9abb661c4ae8b3 100644
--- a/modules/50_damages/DiceLike/declarations.gms
+++ b/modules/50_damages/DiceLike/declarations.gms
@@ -4,7 +4,13 @@
 *** |  AGPL-3.0, you are granted additional permissions described in the
 *** |  REMIND License Exception, version 1.0 (see LICENSE file).
 *** |  Contact: remind@pik-potsdam.de
+*** SOF ./modules/50_damages/DiceLike/declarations.gms
 parameters
 p50_damageFuncCoef1			"damage function coefficient, linear in temperature"
 p50_damageFuncCoef2 			"damage function coefficient, quadratic in temperture"
 ;
+
+positive variable
+vm_damageFactor(ttot,all_regi)      "damage factor reducing GDP"
+;
+*** EOF ./modules/50_damages/DiceLike/declarations.gms
diff --git a/modules/50_damages/off/declarations.gms b/modules/50_damages/off/declarations.gms
new file mode 100644
index 0000000000000000000000000000000000000000..dea6d758d1441423be0db207919b74fabdd583a4
--- /dev/null
+++ b/modules/50_damages/off/declarations.gms
@@ -0,0 +1,11 @@
+*** |  (C) 2006-2019 Potsdam Institute for Climate Impact Research (PIK)
+*** |  authors, and contributors see CITATION.cff file. This file is part
+*** |  of REMIND and licensed under AGPL-3.0-or-later. Under Section 7 of
+*** |  AGPL-3.0, you are granted additional permissions described in the
+*** |  REMIND License Exception, version 1.0 (see LICENSE file).
+*** |  Contact: remind@pik-potsdam.de
+*** SOF ./modules/50_damages/off/declarations.gms
+positive variable
+vm_damageFactor(ttot,all_regi)      "damage factor reducing GDP"
+;
+*** EOF ./modules/50_damages/off/declarations.gms
diff --git a/modules/50_damages/off/realization.gms b/modules/50_damages/off/realization.gms
index 1db5be04680fb06f3d5573228a5ca1be579f353f..af494173342dc89198d68b6cb760fe90297a06ab 100644
--- a/modules/50_damages/off/realization.gms
+++ b/modules/50_damages/off/realization.gms
@@ -9,6 +9,7 @@
 *' @description The off-realization of the damage module sets the damage factor on output to 1, meaning no damage.
 
 *####################### R SECTION START (PHASES) ##############################
+$Ifi "%phase%" == "declarations" $include "./modules/50_damages/off/declarations.gms"
 $Ifi "%phase%" == "bounds" $include "./modules/50_damages/off/bounds.gms"
 *######################## R SECTION END (PHASES) ###############################
 *** EOF ./modules/50_damages/off.gms
diff --git a/scripts/output/comparison/compareScenarios.R b/scripts/output/comparison/compareScenarios.R
index 449801cca4178f27e618ce011553f74194abc8b9..4019b2c2ff2d9094f29a3d423dd6fefd46b90e33 100644
--- a/scripts/output/comparison/compareScenarios.R
+++ b/scripts/output/comparison/compareScenarios.R
@@ -52,7 +52,8 @@ start_comp <- function(outputdirs,shortTerm,outfilename) {
   cat("Starting ",jobname,"\n")
   on_cluster <- file.exists("/p/projects/")
   if (on_cluster) {
-    system(paste0("srun --qos=standby --job-name=",jobname," --output=",jobname,".out --error=",jobname,".err --mail-type=END --time=200 --mem-per-cpu=8000 Rscript scripts/utils/run_compareScenarios.R outputdirs=",paste(outputdirs,collapse=",")," shortTerm=",shortTerm," outfilename=",jobname," &"))
+    clcom <- paste0("sbatch --qos=standby --job-name=",jobname," --output=",jobname,".out --error=",jobname,".err --mail-type=END --time=200 --mem-per-cpu=8000 --wrap=\"Rscript scripts/utils/run_compareScenarios.R outputdirs=",paste(outputdirs,collapse=",")," shortTerm=",shortTerm," outfilename=",jobname,"\"")
+    system(clcom)
   } else {
     outfilename    <- jobname
     tmp.env <- new.env()
diff --git a/scripts/start/prepare_and_run.R b/scripts/start/prepare_and_run.R
index a1346dab09f3c020da84b80c2dc0dc83bbbf683b..320e62edbbf20852534062afda6aafdf8f283e12 100644
--- a/scripts/start/prepare_and_run.R
+++ b/scripts/start/prepare_and_run.R
@@ -765,7 +765,7 @@ prepare_and_run <- function() {
   # In case there are no subsequent runs (or it's coupled runs), the file contains only 
   # a small message.
 
-  subseq_start_file  <- paste0(cfg$results_folder,"/start_subsequentruns.R")
+  subseq_start_file  <- paste0(cfg$results_folder,"/start_subsequentruns_manually.R")
 
   if(no_subsequent_runs){
     write("cat('\nNo subsequent run was set for this scenario\n')",file=subseq_start_file)
@@ -776,6 +776,7 @@ prepare_and_run <- function() {
     for(run in seq(1,length(cfg$subsequentruns))){
       filetext <- paste0(filetext,"\n")
       filetext <- paste0(filetext,"load('",cfg$subsequentruns[run],".RData')\n")
+      #filetext <- paste0(filetext,"cfg$results_folder <- 'output/:title::date:'\n")
       filetext <- paste0(filetext,"cat('",cfg$subsequentruns[run],"')\n")
       filetext <- paste0(filetext,"submit(cfg)\n")
     }
diff --git a/scripts/start/submit.R b/scripts/start/submit.R
index 25d3db720391d8b7b0cd6fcfb76c63975127e605..ccc81c54aa367247828ef357ae059a3ec0cb8b2f 100644
--- a/scripts/start/submit.R
+++ b/scripts/start/submit.R
@@ -15,42 +15,44 @@
 
 submit <- function(cfg) {
   
-  # Create name of output folder and output folder itself
+  # Generate name of output folder and create the folder
   date <- format(Sys.time(), "_%Y-%m-%d_%H.%M.%S")
   cfg$results_folder <- gsub(":date:", date, cfg$results_folder, fixed = TRUE)
   cfg$results_folder <- gsub(":title:", cfg$title, cfg$results_folder, fixed = TRUE)
   # Create output folder
+  cat("   Creating results folder",cfg$results_folder,"\n")
   if (!file.exists(cfg$results_folder)) {
     dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
   } else if (!cfg$force_replace) {
     stop(paste0("Results folder ",cfg$results_folder," could not be created because it already exists."))
   } else {
-    cat("Deleting results folder because it alreay exists:",cfg$results_folder,"\n")
+    cat("    Deleting results folder because it alreay exists:",cfg$results_folder,"\n")
     unlink(cfg$results_folder, recursive = TRUE)
     dir.create(cfg$results_folder, recursive = TRUE, showWarnings = FALSE)
   }
   
-  # save main folder
+  # remember main folder
   cfg$remind_folder <- getwd()
- 
-  # save the cfg data before moving it into the results folder
-  cat("Writing cfg to file\n")
-  save(cfg,file=paste0(cfg$title,".RData"))
+  
+  # Save the cfg (with the updated name of the result folder) into the results folder. 
+  # Do not save the new name of the results folder to the .RData file in REMINDs main folder, because it 
+  # might be needed to restart subsequent runs manually and should not contain the time stamp in this case.
+  filename <- paste0(cfg$results_folder,"/config.Rdata")
+  cat("   Writing cfg to file",filename,"\n")
+  save(cfg,file=filename)
   
   # Copy files required to confiugre and start a run
-  filelist <- c("config.Rdata" = paste0(cfg$title,".RData"),
-                "prepare_and_run.R" = "scripts/start/prepare_and_run.R")
+  filelist <- c("prepare_and_run.R" = "scripts/start/prepare_and_run.R")
   .copy.fromlist(filelist,cfg$results_folder)
   
-  # remove config in main folder (after copying into results folder)
-  file.remove(paste0(cfg$title,".RData"))
+  # Do not remove .RData files from REMIND main folder because they are needed in case you need to manually restart subsequent runs.
 
-  # change to run folder
+  # Change to run folder
   setwd(cfg$results_folder)
   on.exit(setwd(cfg$remind_folder))
-
+  
   # send prepare_and_run.R to cluster 
-  cat("Executing prepare_and_run.R for",cfg$title,"\n")
+  cat("   Executing prepare_and_run.R for",cfg$results_folder,"\n")
   if(cfg$slurmConfig=="direct") {
     log <- format(Sys.time(), paste0(cfg$title,"-%Y-%H-%M-%S-%OS3.log"))
     system("Rscript prepare_and_run.R")
diff --git a/start.R b/start.R
index fde2696c5e8596d7ddca802e6e55078004bd817a..854bb33a8d494fed43681241f62a2f9e16f5d88a 100644
--- a/start.R
+++ b/start.R
@@ -15,7 +15,7 @@ configure_cfg <- function(icfg, iscen, iscenarios, isettings) {
 
     # Edit run title
     icfg$title <- iscen
-    cat("\n", iscen, "\n")
+    cat("   Configuring cfg for", iscen,"\n")
 
     # Edit main file of model
     if( "model" %in% names(iscenarios)){
@@ -101,10 +101,12 @@ config.file <- argv[1]
 if ('--testOneRegi' %in% argv) {
   testOneRegi <- TRUE
   config.file <- NA
+} else {
+  testOneRegi <- FALSE
 }
 
 if (!is.na(config.file)) {
-  cat(paste("reading config file", config.file, "\n"))
+  cat(paste("\nReading config file", config.file, "\n"))
 
   # Read-in the switches table, use first column as row names
   settings <- read.csv2(config.file, stringsAsFactors = FALSE, row.names = 1, comment.char = "#", na.strings = "")
@@ -137,25 +139,31 @@ for (scen in rownames(scenarios)) {
     cfg$results_folder   <- 'output/testOneRegi'
 
     # delete existing Results directory
-    unlink('output/testOneRegi', recursive = TRUE)
+    cfg$force_replace    <- TRUE
   }
 
+  cat("\n",scen,"\n")
+
   # configure cfg based on settings from csv if provided
   if (!is.na(config.file)) {
-
-  cfg <- configure_cfg(cfg, scen, scenarios, settings)
-
-  # Directly start runs that have a gdx file location given as path_gdx_ref or where this field is empty
-  start_now <- (substr(scenarios[scen,"path_gdx_ref"], nchar(scenarios[scen,"path_gdx_ref"])-3, nchar(scenarios[scen,"path_gdx_ref"])) == ".gdx"
-               | is.na(scenarios[scen,"path_gdx_ref"]))
+    cfg <- configure_cfg(cfg, scen, scenarios, settings)
+    # Directly start runs that have a gdx file location given as path_gdx_ref or where this field is empty
+    start_now <- (substr(scenarios[scen,"path_gdx_ref"], nchar(scenarios[scen,"path_gdx_ref"])-3, nchar(scenarios[scen,"path_gdx_ref"])) == ".gdx"
+                 | is.na(scenarios[scen,"path_gdx_ref"]))
   }
-
+  
   # save the cfg data for later start of subsequent runs (after preceding run finished)
-  cat("Writing cfg to file\n")
-  save(cfg,file=paste0(scen,".RData"))
+  filename <- paste0(scen,".RData")
+  cat("   Writing cfg to file",filename,"\n")
+  save(cfg,file=filename)
 
   if (start_now){
-   cat("Creating and starting: ",cfg$title,"\n")
-   submit(cfg)
-   }
+    # Create results folder and start run
+    submit(cfg)
+    } else {
+    cat("   Waiting for", scenarios[scen,'path_gdx_ref'] ,"\n")
+  }
+
+  if (!identical(cfg$subsequentruns,character(0))) cat("   Subsequent runs:",cfg$subsequentruns,"\n")
+  
 }