diff --git a/.ci/prfilter b/.ci/prfilter
index 78eea80c..73d4396e 100755
--- a/.ci/prfilter
+++ b/.ci/prfilter
@@ -14,7 +14,6 @@ THE_BIG_LIST_OF_NAUGHTY_FILES = list(map(pathlib.Path, [
     # only when they are a part of the current pull request.
     #
 
-    # for pylint
     'Documentation/conf.py',
     'LibOS/shim/test/ltp/contrib/conf_lint.py',
     'LibOS/shim/test/ltp/contrib/conf_merge.py',
@@ -37,17 +36,6 @@ THE_BIG_LIST_OF_NAUGHTY_FILES = list(map(pathlib.Path, [
     'Pal/src/host/Linux/pal-gdb.py',
     'Scripts/regression.py',
     'Tools',
-
-    # for shellcheck
-    'Examples/bash/scripts/bash_test.sh',
-    'Examples/common_tools/benchmark-http.sh',
-    'Examples/python-simple/run-tests.sh',
-    'LibOS/shim/test/native',
-    'Pal/src/host/Linux-SGX/debugger/gdb',
-    'Scripts/list-all-graphene.sh',
-    'Scripts/memusg',
-    '.ci/run-pylint',
-    '.ci/run-shellcheck',
 ]))
 
 def get_diff_ranges(ref=DEFAULT_REF):
diff --git a/.ci/run-shellcheck b/.ci/run-shellcheck
index 82d4dbb6..a8b4df2c 100755
--- a/.ci/run-shellcheck
+++ b/.ci/run-shellcheck
@@ -8,7 +8,6 @@ shellcheck "$@" \
     Examples/bash/scripts/bash_test.sh \
     Examples/common_tools/benchmark-http.sh \
     Examples/python-simple/run-tests.sh \
-    LibOS/shim/test/native/*.sh \
     Pal/src/host/Linux-SGX/debugger/gdb \
     Runtime/pal_loader \
     Scripts/clean-check \
@@ -16,7 +15,5 @@ shellcheck "$@" \
     Scripts/clean-check-test-copy \
     Scripts/download \
     Scripts/gitignore-test \
-    Scripts/list-all-graphene.sh \
-    Scripts/memusg \
     .ci/run-pylint \
     .ci/run-shellcheck
diff --git a/Examples/bash/scripts/bash_test.sh b/Examples/bash/scripts/bash_test.sh
index e3396596..e8687099 100755
--- a/Examples/bash/scripts/bash_test.sh
+++ b/Examples/bash/scripts/bash_test.sh
@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
 
 times=$1
-[ $times -gt 0 2> /dev/null ] || times=300
+[ "$times" -gt 0 ] 2>/dev/null || times=300
 
-for (( c=1; c<=$times; c++ ))
+for (( c=1; c<=times; c++ ))
 do
 	echo "hello $c"
 	cp somefile testdir/somefile
diff --git a/Examples/common_tools/benchmark-http.sh b/Examples/common_tools/benchmark-http.sh
index 1e2c9761..fb5340f9 100755
--- a/Examples/common_tools/benchmark-http.sh
+++ b/Examples/common_tools/benchmark-http.sh
@@ -16,16 +16,16 @@ CONCURRENCY_LIST=${CONCURRENCY_LIST:-"1 2 4 8 16 32 64 128 256"}
 OPTIONS="-k"
 RESULT=result-$(date +%y%m%d-%H%M%S)
 
-touch $RESULT
+touch "$RESULT"
 
 RUN=0
-while [ $RUN -lt $LOOP ]
+while [ $RUN -lt "$LOOP" ]
 do
     for CONCURRENCY in $CONCURRENCY_LIST
     do
         rm -f OUTPUT
         echo "ab $OPTIONS -n $REQUESTS -c $CONCURRENCY $DOWNLOAD_HOST/$DOWNLOAD_FILE"
-        ab $OPTIONS -n $REQUESTS -c $CONCURRENCY $DOWNLOAD_HOST/$DOWNLOAD_FILE > OUTPUT || exit $?
+        ab $OPTIONS -n $REQUESTS -c "$CONCURRENCY" "$DOWNLOAD_HOST/$DOWNLOAD_FILE" > OUTPUT || exit $?
 
         sleep 5
 
@@ -36,14 +36,14 @@ do
         LATENCIES[$CONCURRENCY]="${LATENCIES[$CONCURRENCY]} $LATENCY"
         echo "concurrency=$CONCURRENCY, throughput=$THROUGHPUT, latency=$LATENCY, failed=$FAILED"
     done
-    RUN=$(expr $RUN + 1)
+    (( RUN++ ))
 done
 
 for CONCURRENCY in $CONCURRENCY_LIST
 do
-    THROUGHPUT=$(echo ${THROUGHPUTS[$CONCURRENCY]} | tr " " "\n" | sort -n | awk '{a[NR]=$0}END{if(NR%2==1)print a[int(NR/2)+1];else print(a[NR/2-1]+a[NR/2])/2}')
-    LATENCY=$(echo ${LATENCIES[$CONCURRENCY]} | tr " " "\n" | sort -n | awk '{a[NR]=$0}END{if(NR%2==1)print a[int(NR/2)+1];else print(a[NR/2-1]+a[NR/2])/2}')
-    echo "$THROUGHPUT,$LATENCY" >> $RESULT
+    THROUGHPUT=$(echo "${THROUGHPUTS[$CONCURRENCY]}" | tr " " "\n" | sort -n | awk '{a[NR]=$0}END{if(NR%2==1)print a[int(NR/2)+1];else print(a[NR/2-1]+a[NR/2])/2}')
+    LATENCY=$(echo "${LATENCIES[$CONCURRENCY]}" | tr " " "\n" | sort -n | awk '{a[NR]=$0}END{if(NR%2==1)print a[int(NR/2)+1];else print(a[NR/2-1]+a[NR/2])/2}')
+    echo "$THROUGHPUT,$LATENCY" >> "$RESULT"
 done
 
 echo "Result file: $RESULT"
diff --git a/Examples/python-simple/run-tests.sh b/Examples/python-simple/run-tests.sh
index 8db46bfe..97436536 100755
--- a/Examples/python-simple/run-tests.sh
+++ b/Examples/python-simple/run-tests.sh
@@ -24,5 +24,5 @@ echo -e "\n\nRunning HTTP client test-http.py:"
 wget -q http://localhost:8005/ -O OUTPUT2
 echo >> OUTPUT2  # include newline since wget doesn't add it
 diff -q OUTPUT1 OUTPUT2 && echo "[ Success 3/3 ]"
-kill `cat server.PID`
+kill "$(cat server.PID)"
 rm -f OUTPUT1 OUTPUT2 server.PID
diff --git a/Jenkinsfiles/Linux b/Jenkinsfiles/Linux
index 98daad07..227448ce 100644
--- a/Jenkinsfiles/Linux
+++ b/Jenkinsfiles/Linux
@@ -8,8 +8,7 @@ pipeline {
                 stage('Lint') {
                     steps {
                         sh '''
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-18.04 b/Jenkinsfiles/Linux-18.04
index c5b35cc1..f8878fa9 100644
--- a/Jenkinsfiles/Linux-18.04
+++ b/Jenkinsfiles/Linux-18.04
@@ -11,8 +11,7 @@ pipeline {
                             ./.ci/run-pylint -f text || :
                             ./.ci/run-pylint -f json | ./.ci/prfilter
 
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-Debug b/Jenkinsfiles/Linux-Debug
index 52f78083..9d84c5af 100644
--- a/Jenkinsfiles/Linux-Debug
+++ b/Jenkinsfiles/Linux-Debug
@@ -8,8 +8,7 @@ pipeline {
                 stage('Lint') {
                     steps {
                         sh '''
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-Debug-18.04 b/Jenkinsfiles/Linux-Debug-18.04
index 4cbbac51..42568048 100644
--- a/Jenkinsfiles/Linux-Debug-18.04
+++ b/Jenkinsfiles/Linux-Debug-18.04
@@ -11,8 +11,7 @@ pipeline {
                             ./.ci/run-pylint -f text || :
                             ./.ci/run-pylint -f json | ./.ci/prfilter
 
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-SGX b/Jenkinsfiles/Linux-SGX
index bd9914c0..b7abc812 100644
--- a/Jenkinsfiles/Linux-SGX
+++ b/Jenkinsfiles/Linux-SGX
@@ -9,8 +9,7 @@ pipeline {
                 stage('Lint') {
                     steps {
                         sh '''
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-SGX-18.04 b/Jenkinsfiles/Linux-SGX-18.04
index 2d888988..853ac65b 100644
--- a/Jenkinsfiles/Linux-SGX-18.04
+++ b/Jenkinsfiles/Linux-SGX-18.04
@@ -12,8 +12,7 @@ pipeline {
                             ./.ci/run-pylint -f text || :
                             ./.ci/run-pylint -f json | ./.ci/prfilter
 
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-SGX-18.04-apps b/Jenkinsfiles/Linux-SGX-18.04-apps
index 4f36b436..52c5c70a 100644
--- a/Jenkinsfiles/Linux-SGX-18.04-apps
+++ b/Jenkinsfiles/Linux-SGX-18.04-apps
@@ -12,8 +12,7 @@ pipeline {
                             ./.ci/run-pylint -f text || :
                             ./.ci/run-pylint -f json | ./.ci/prfilter
 
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/Jenkinsfiles/Linux-SGX-apps b/Jenkinsfiles/Linux-SGX-apps
index eeb3e573..1e04336a 100644
--- a/Jenkinsfiles/Linux-SGX-apps
+++ b/Jenkinsfiles/Linux-SGX-apps
@@ -9,8 +9,7 @@ pipeline {
                 stage('Lint') {
                     steps {
                         sh '''
-                            ./.ci/run-shellcheck || :
-                            ./.ci/run-shellcheck -f json | ./.ci/prfilter
+                            ./.ci/run-shellcheck
                         '''
                     }
                 }
diff --git a/LibOS/shim/test/native/Makefile b/LibOS/shim/test/native/Makefile
index e1e16428..8706ba10 100644
--- a/LibOS/shim/test/native/Makefile
+++ b/LibOS/shim/test/native/Makefile
@@ -34,7 +34,6 @@ c_executables = \
 	pipe_latency \
 	readdir \
 	rename \
-	script \
 	sem \
 	sleep \
 	socketpair \
@@ -54,7 +53,6 @@ manifests = \
 	manifest \
 	exec_fork.manifest \
 	ls.manifest \
-	script.manifest \
 	static.manifest
 
 exec_target = \
diff --git a/LibOS/shim/test/native/script.c b/LibOS/shim/test/native/script.c
deleted file mode 100644
index 98c55acb..00000000
--- a/LibOS/shim/test/native/script.c
+++ /dev/null
@@ -1,17 +0,0 @@
-#define _XOPEN_SOURCE 700
-#include <errno.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <unistd.h>
-
-int main(int argc, const char** argv, const char** envp) {
-    int newfd = dup(1);
-    char fd_argv[4];
-    snprintf(fd_argv, 4, "%d", newfd);
-    char* const new_argv[] = {"./script1.sh", fd_argv, NULL};
-
-    setenv("IN_EXECVE", "1", 1);
-
-    execv(new_argv[0], new_argv);
-    return 1;
-}
diff --git a/LibOS/shim/test/native/script.manifest.template b/LibOS/shim/test/native/script.manifest.template
deleted file mode 100644
index 82b00ed2..00000000
--- a/LibOS/shim/test/native/script.manifest.template
+++ /dev/null
@@ -1,28 +0,0 @@
-loader.preload = file:$(SHIMPATH)
-loader.env.LD_LIBRARY_PATH = /lib
-loader.debug_type = inline
-loader.syscall_symbol = syscalldb
-loader.insecure__use_cmdline_argv = 1
-
-fs.mount.lib.type = chroot
-fs.mount.lib.path = /lib
-fs.mount.lib.uri = file:$(LIBCDIR)
-
-fs.mount.bin.type = chroot
-fs.mount.bin.path = /bin
-fs.mount.bin.uri = file:/bin
-
-sys.brk.max_size = 32M
-sys.stack.size = 4M
-
-sgx.trusted_files.ld = file:$(LIBCDIR)/ld-linux-x86-64.so.2
-sgx.trusted_files.libc = file:$(LIBCDIR)/libc.so.6
-sgx.trusted_files.libdl = file:$(LIBCDIR)/libdl.so.2
-sgx.trusted_files.libm = file:$(LIBCDIR)/libm.so.6
-sgx.trusted_files.libpthread = file:$(LIBCDIR)/libpthread.so.0
-
-sgx.trusted_files.script1_sh = file:script1.sh
-sgx.trusted_files.script2_sh = file:script2.sh
-sgx.trusted_files.script3_sh = file:script3.sh
-sgx.trusted_files.helloworld = file:helloworld
-sgx.trusted_children.helloworld = file:helloworld.sig
diff --git a/LibOS/shim/test/native/script1.sh b/LibOS/shim/test/native/script1.sh
deleted file mode 100644
index b479d977..00000000
--- a/LibOS/shim/test/native/script1.sh
+++ /dev/null
@@ -1 +0,0 @@
-#!/script2.sh
diff --git a/LibOS/shim/test/native/script2.sh b/LibOS/shim/test/native/script2.sh
deleted file mode 100644
index b0b41da9..00000000
--- a/LibOS/shim/test/native/script2.sh
+++ /dev/null
@@ -1 +0,0 @@
-#!/script3.sh
diff --git a/LibOS/shim/test/native/script3.sh b/LibOS/shim/test/native/script3.sh
deleted file mode 100644
index 46a44c0a..00000000
--- a/LibOS/shim/test/native/script3.sh
+++ /dev/null
@@ -1 +0,0 @@
-#!/helloworld
diff --git a/Pal/src/host/Linux-SGX/debugger/gdb b/Pal/src/host/Linux-SGX/debugger/gdb
index 6209d084..77e6c235 100755
--- a/Pal/src/host/Linux-SGX/debugger/gdb
+++ b/Pal/src/host/Linux-SGX/debugger/gdb
@@ -1,6 +1,6 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-DIR=$(dirname $(readlink -f ${BASH_SOURCE[0]}))
+DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
 GDB_SCRIPT=$DIR/pal-gdb.py
 GDB_SO=$DIR/sgx_gdb.so
 if [ -z "$INSIDE_EMACS" ]; then
diff --git a/Runtime/pal_loader b/Runtime/pal_loader
index 8cde4470..9e483929 100755
--- a/Runtime/pal_loader
+++ b/Runtime/pal_loader
@@ -72,10 +72,6 @@ if [ "$PERF" == "1" ]; then
 	PREFIX=(perf stat)
 fi
 
-if [ "$MEMUSG" == "1" ]; then
-	PREFIX=("$RUNTIME_DIR/../Scripts/memusg")
-fi
-
 while [ "$1" != "" ];
 do
 	if [ "$MANIFEST" == "" ]; then
diff --git a/Scripts/list-all-graphene.sh b/Scripts/list-all-graphene.sh
deleted file mode 100755
index 0b222a7c..00000000
--- a/Scripts/list-all-graphene.sh
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env bash
-
-ID=`id -u`
-PGIDS=`ps -a -o pgid,command | tail -n +2 | \
-	awk "{ if (\\\$2 ~ /\\/pal\$/ ) print \\\$1 }" | uniq`
-
-NONE=1
-for PGID in $PGIDS
-do
-	NONE=0
-	ps -p $PGID -o pid,args 2> /dev/null | tail -n +2
-done
-
-if [ "$NONE" = "1" ]; then
-	echo "no graphene instance"
-	exit 0
-fi
-
-echo -n "choose intance(s): "
-read SELECT_PGIDS
-
-DO_KILL=0
-for CMD in $SELECT_PGIDS
-do
-	if [ "$CMD" = "kill" ]; then
-		SELECT_PGIDS=${SELECT_PGIDS:4}
-		DO_KILL=1
-	fi
-	break
-done
-
-do_list()
-{
-	PGID=$1
-	echo "instance $PGID:"
-	PIDS=`ps -a -o pgid,pid --sort=start_time 2> /dev/null | tail -n +2 | \
-		awk "{ if (\\\$1 == $PGID) print \\\$2 }"`
-
-	CNT=1
-	for PID in $PIDS
-	do
-		STAT=`ps -a -p $PID -o stat | tail -n +2`
-		if [[ $STAT == Z* ]]; then
-			printf "    %3d: process %5d (DEAD):" $CNT $PID
-		else
-			printf "    %3d: process %5d       :" $CNT $PID
-		fi
-		for TASK in /proc/$PID/task/*
-		do
-			printf " %5d" ${TASK##*/}
-		done
-		echo
-		CNT=`expr $CNT + 1`
-	done
-}
-
-do_kill()
-{
-	PGID=$1
-	PIDS=`ps -a -o pgid,pid 2> /dev/null | tail -n +2 | \
-		awk "{ if (\\\$1 == $PGID) print \\\$2 }"`
-	kill -9 $PGID $PIDS
-}
-
-NONE=1
-for PGID in $SELECT_PGIDS
-do
-	if [ "$DO_KILL" = "1" ]; then
-		do_kill $PGID
-	else
-		do_list $PGID
-	fi
-	NONE=0
-done
-
-if [ "$NONE" = "1" ]; then
-	for PGID in $PGIDS
-	do
-		if [ "$DO_KILL" = "1" ]; then
-			do_kill $PGID
-		else
-			do_list $PGID
-		fi
-	done
-fi
diff --git a/Scripts/memusg b/Scripts/memusg
deleted file mode 100755
index e351431e..00000000
--- a/Scripts/memusg
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env bash
-# memusg -- Measure memory usage of processes
-# Usage: memusg COMMAND [ARGS]...
-#
-# Author: Jaeho Shin <netj@sparcs.org>
-# Created: 2010-08-16
-set -um
-
-# check input
-[ $# -gt 0 ] || { sed -n '2,/^#$/ s/^# //p' <"$0"; exit 1; }
-
-# TODO support more options: peak, footprint, sampling rate, etc.
-
-pgid=`ps -o pgid= $$`
-
-command="$@"
-
-# make sure we're in a separate process group
-if [ $pgid = $(ps -o pgid= $(ps -o ppid= $$)) ]; then
-    cmd=
-    set -- "$0" "$@"
-    for a; do cmd+="'${a//"'"/"'\\''"}' "; done
-    exec bash -i -c "$cmd"
-fi
-
-# detect operating system and prepare measurement
-case `uname` in
-    Darwin|*BSD) sizes() { /bin/ps -o rss= -g $1; } ;;
-    Linux) sizes() { /bin/ps -o rss= -$1; } ;;
-    *) echo "`uname`: unsupported operating system" >&2; exit 2 ;;
-esac
-
-rm -f "histogram.mem.usg"
-
-# monitor the memory usage in the background.
-(
-peak=0
-while sizes=`sizes $pgid`
-do
-    set -- $sizes
-    sample=$((${@/#/+}))
-    echo "$sample" >> "histogram.mem.usg"
-    let peak="sample > peak ? sample : peak"
-    sleep 0.1
-done
-echo "memusg \`$command\`: peak=$peak kiloBytes" >> "peak.mem.usg"
-) &
-monpid=$!
-
-echo "running: exec $@"
-
-# run the given command
-exec "$@"