diff --git a/bin/read_sos.py b/bin/read_sos.py
old mode 100644
new mode 100755
diff --git a/bin/sos_apocommand b/bin/sos_apocommand
index 904bb944..c1301c4a 100755
--- a/bin/sos_apocommand
+++ b/bin/sos_apocommand
@@ -30,9 +30,10 @@ function usage
 	echo "   -m    MJD"
 	echo " "
 	echo "   -d    Dry run."
-        echo "   -e    FPS mode"
+	echo "   -e    FPS mode"
+	echo "   -a    no cal mode"
 	echo " "
-	echo "All parameters except -d and -e are required, FPS mode is set by default."
+	echo "All parameters except -d, -a, and -e are required, FPS mode is set by default."
 	echo "Normally $execName will be called by sos_runnerd."
     ) >&2
     exit 1
@@ -127,7 +128,7 @@ plugDir=""
 MJD=""
 SOSDir=""
 
-while getopts "f:i:p:l:s:m:a:de" argname; do
+while getopts "f:i:p:l:s:m:ade" argname; do
     case $argname in
 	  f) fitsName=$OPTARG ;;
 	  i) inDir=$OPTARG ;;
diff --git a/bin/sos_aporedo b/bin/sos_aporedo
index efba7f62..b61bfa2c 100755
--- a/bin/sos_aporedo
+++ b/bin/sos_aporedo
@@ -143,7 +143,7 @@ go=false
 FPSmod="T"
 nocal="F"
 
-while getopts "wthrdfm:z:n:g" argname; do
+while getopts "wthrdfm:z:ng" argname; do
     case $argname in
 	  w) doWait=true ;;
 #      X) svnMode=""; svnCheck=true ;;
diff --git a/bin/sos_filesequencer b/bin/sos_filesequencer
index ea3389b6..f26af7b7 100755
--- a/bin/sos_filesequencer
+++ b/bin/sos_filesequencer
@@ -59,7 +59,7 @@ class Config:
 		self.sosdir   = ""
 		self.mjd      = ""
 		self.fps      = "T"
-        self.nocal    = "F"
+		self.nocal    = "F"
 		
 	def __str__(self):
 		return ("fitname:  " + self.fitname + "\n" +
@@ -69,7 +69,7 @@ class Config:
 		        "sosdir:   " + self.sosdir + "\n" +
 		        "mjd:      " + self.mjd + "\n" +
 		        "fps:      " + self.fps + "\n" +
-                "nocal:    " + self.nocal);
+			"nocal:    " + self.nocal);
 
 
 
@@ -110,8 +110,8 @@ def parseCmdLine(args):
 			cfg.mjd = value
 		if opt == "-e":
 			cfg.fps = value
-        if opt == "-a":
-            cfg.nocal = value
+		if opt == "-a":
+			cfg.nocal = value
 	print("Config values: \n" + str(cfg))
 	
 	return cfg
@@ -171,7 +171,7 @@ def processFile(cfg, flavor=""):
 	cmd += " -p " + cfg.plugname
 	cmd += " -l " + cfg.plugpath
 	cmd += " -s " + cfg.sosdir
-    cmd += " -m " + cfg.mjd
+	cmd += " -m " + cfg.mjd
 	if cfg.fps == "T":
 		cmd += " -e "
     if cfg.nocal == "T":
diff --git a/pro/spec2d/prerun_readplugmap.pro b/pro/spec2d/prerun_readplugmap.pro
index cd986b51..4702b7cb 100644
--- a/pro/spec2d/prerun_readplugmap.pro
+++ b/pro/spec2d/prerun_readplugmap.pro
@@ -968,7 +968,6 @@ function prerun_readplugmap, plugfile, outfile, plugdir=plugdir, apotags=apotags
     endif else begin
         PMobjName='FIBERMAP'
         maptype='confSummary'
-        print,plugfile, plugdir
         if keyword_set(plugdir) then begin
             thisfile = (findfile(djs_filepath(plugfile, root_dir=plugdir, subdir='*'), count=ct))[0]
         endif else begin
diff --git a/pro/spec2d/readplugmap.pro b/pro/spec2d/readplugmap.pro
index a2665608..2c87c489 100644
--- a/pro/spec2d/readplugmap.pro
+++ b/pro/spec2d/readplugmap.pro
@@ -106,11 +106,12 @@ end
 
 ;------------------------------------------------------------------------------
 
-function get_parent_plugfile, pf, cloned_from, plugdir
+function get_parent_plugfile, pf, cloned_from, plugdir=plugdir
    ;plugdir = file_dirname(file_dirname(pf),/MARK_DIRECTORY)
-   if plugdir eq './' then begin
+   if not keyword_set(plugdir) then begin
+      thisplug = FILE_DIRNAME(FILE_DIRNAME(pf))
       confile = (findfile(filepath('confSummaryF-'+strtrim(cloned_from,2)+'.par',$
-                                    root_dir='./'), count=ct))[0]
+                                    root_dir=thisplug, subdir='*'), count=ct))[0]
       if (ct ne 0) then ppf = 'confSummaryF-'+strtrim(cloned_from,2)+'.par' $
                    else ppf = 'confSummary-'+strtrim(cloned_from,2)+'.par'
       pfp = ppf
@@ -162,9 +163,9 @@ function readplugmap, plugfile, spectrographid, plugdir=plugdir, savdir=savdir,
     hdr = ['cut']
     plugmap = []
     fibermask = [-100]
-    plugdir_raw = plugdir
+    if keyword_set(plugdir) then plugdir_raw = plugdir
     foreach pf, plugfile do begin
-        plugdir = plugdir_raw
+        if keyword_set(plugdir_raw) then plugdir = plugdir_raw
         if keyword_set(plugdir) then $
             yanny_read, (findfile(djs_filepath(pf, root_dir=plugdir, subdir='*'), count=ct))[0], junk, hdr=filehdr, /anonymous $
         else yanny_read, pf, junk, hdr=filehdr, /anonymous
@@ -176,7 +177,7 @@ function readplugmap, plugfile, spectrographid, plugdir=plugdir, savdir=savdir,
             cloned_to_conf = yanny_par(filehdr, 'configuration_id')
             cloned_to_design = yanny_par(filehdr, 'design_id')
             if (( cloned_from_conf NE '-999') AND (cnt NE 0)) then begin
-                ppf = get_parent_plugfile(pf,cloned_from_conf,plugdir)
+                ppf = get_parent_plugfile(pf,cloned_from_conf,plugdir=plugdir)
             endif else ppf = pf
         endelse
 
@@ -217,7 +218,9 @@ function readplugmap, plugfile, spectrographid, plugdir=plugdir, savdir=savdir,
                                     'configuration_id '+string(cloned_to_conf)
                         hdr1[where(strmatch(hdr1, '*design_id*',/FOLD_CASE) EQ 1)] = $
                                     'design_id '+strtrim(cloned_to_design,2)
-                        hdr1=[hdr1,'cloned_from '+strtrim(cloned_from_conf,2)]
+                        hdr1[where(strmatch(hdr1, '*cloned_from*',/FOLD_CASE) EQ 1)] = $
+                                    'cloned_from '+strtrim(cloned_from_conf,2)
+;                        hdr1=[hdr1,'cloned_from '+strtrim(cloned_from_conf,2)]
                     endif
                     hdrf = yanny_to_fits_hdr(hdr1)
                     sxaddpar, hdrf, 'EXTNAME', file_basename(pf), ' Complete Plugmap/confSummary'