From 62d58cae7ce152b4bb9771d307a4185af25ae10d Mon Sep 17 00:00:00 2001
From: Gobbo <gobbo_a@sf-lc8.psi.ch>
Date: Mon, 1 Sep 2025 16:42:37 +0200
Subject: [PATCH] Fix arguments removal (PShell 2.x compatibility)

---
 pshell | 118 ++++++++++++++++++++-------------------------------------
 1 file changed, 42 insertions(+), 76 deletions(-)

diff --git a/pshell b/pshell
index 87f85ab..9776aea 100755
--- a/pshell
+++ b/pshell
@@ -49,92 +49,59 @@ case $i in
 esac
 done
 
-
-
 #Parse JVM arguments, Pshell version and JEP option
 export PSHELL_VER=default
 export VER_SUFFIX=
 export JVM_ARGS=
-export JVM_UCP=
-#export JAVA_VER=/opt/gfa/java/openjdk-1.8.0_40
-#export JAVA_VER=/opt/gfa/java/jdk1.8.0_72
+export UCP=
 export JAVA_VER=/opt/gfa/java/openjdk-12_32
-#export JEP=
 
-for i in "$@"
-do
-case $i in
+
+# Collect remaining args safely
+REMAINING_ARGS=""
+
+while [ $# -gt 0 ]; do
+  case $1 in
     -jvmarg=*)
-	JVM_ARGS="${i#*=}"
-	#echo 'JVM args:' ${JVM_ARGS}
-    	#shift 
-    ;;
-
+      JVM_ARGS="${1#*=}"
+      #echo "JVM args: $JVM_ARGS"
+      ;;
     -ucp=*)
-        UCP="${i#*=}"
-        #echo 'UCP:' ${UCP}
-        #shift
-    ;;
-
-    -version=*|--version=*)
-	export PSHELL_VER="${i#*=}"
-	#echo "Using  version " ${PSHELL_VER}
-	#shift
-    ;;
-
-    -test)	
-	export PSHELL_VER=testing
-	#echo "Using testing version"
-    	#shift 
-    ;;
-
+      UCP="${1#*=}"
+      #echo "UCP: $UCP"
+      ;;
+    -version=*)
+      export PSHELL_VER="${1#*=}"
+      #echo "Using version $PSHELL_VER"
+      ;;
+    -test)
+      export PSHELL_VER="testing"
+      #echo "Using testing version"
+      ;;
     -last)
-	export PSHELL_VER=latest
-	#echo "Using latest version"
-       #shift 
-    ;;
-
+      export PSHELL_VER="latest"
+      #echo "Using latest version"
+      ;;
     -light)
-        export VER_SUFFIX=-light
-        #echo "Using build type " ${VER_SUFFIX}
-       #shift 
-    ;;    
-
-    -javaver=*|--javaver=*)
-	export JAVA_VER="${i#*=}"
-	echo "Using  Java version " ${JAVA_VER}
-	#shift
-    ;;
-
-#    -py2)
-#	JEP=2
-#	echo "Setting Python 2 for JEP"
-#        shift 
-#    ;;
-
-#    -py3)
-#	JEP=3
-#	echo "Setting Python 3 for JEP"
-#        shift 
-#    ;;
-
-    *)    # unknown option            
-    ;;
-esac
+      export VER_SUFFIX="-light"
+      #echo "Using build type $VER_SUFFIX"
+      ;;
+    -javaver=*)
+      export JAVA_VER="${1#*=}"
+      #echo "Using Java version $JAVA_VER"
+      ;;
+    *)
+      REMAINING_ARGS="$REMAINING_ARGS \"$1\""
+      ;;
+  esac
+  shift
 done
 
-#echo $@
+#echo "Remaining args: $REMAINING_ARGS"
+
+# Final exec (safe with spaces)
+eval set -- $REMAINING_ARGS
 
-#Parse Pshell version
-#if [[ $@ == **-test** ]] ; then
-#	echo "Using testing version"
-#	export PSHELL_VER=testing
-#else
-# if [[ $@ == **-last** ]] ; then
-#	echo "Using latest version"
-#	export PSHELL_VER=latest
-# fi
-#fi
 
 if [[ $VER_SUFFIX != "" ]] ; then
         PSHELL_VER=${PSHELL_VER}${VER_SUFFIX}
@@ -154,9 +121,8 @@ fi
 
 #Standard startup
 if [[ $@ != **-py**  ||  $VER_SUFFIX == "-light" ]] ; then
-#if [[ $JEP == "" ]] ; then
 if [[ $UCP == "" ]] ; then
-	${JAVA_VER}/bin/java ${JVM_EARGS} ${JVM_ARGS} -jar /opt/gfa/pshell/${PSHELL_VER} ${1+"$@"}
+	${JAVA_VER}/bin/java ${JVM_EARGS} ${JVM_ARGS} -jar /opt/gfa/pshell/${PSHELL_VER} "$@"
 	exit  
 fi
 fi
@@ -218,5 +184,5 @@ if [[ $UCP != "" ]] ; then
 fi
 
 export PATH=${PYTHONHOME}/bin:$CLEAN_PATH
-${JAVA_VER}/bin/java  ${JVM_EARGS} ${JVM_ARGS} -cp ${UCP}/opt/gfa/pshell/${PSHELL_VER}:${JEP_JAR} ch.psi.pshell.ui.App ${1+"$@"}
+${JAVA_VER}/bin/java  ${JVM_EARGS} ${JVM_ARGS} -cp ${UCP}/opt/gfa/pshell/${PSHELL_VER}:${JEP_JAR} ch.psi.pshell.ui.App "$@"