From 951c3605b89f43a228cd6573e84d413617eb77b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Just?= <rjust@users.noreply.github.com>
Date: Fri, 6 Sep 2024 11:18:49 -0700
Subject: [PATCH] Consolidate version-3 and Java-11 branches (#594)

---------

Co-authored-by: Michael Ernst <mernst@cs.washington.edu>
---
 .github/workflows/ci.yml                      |  3 +
 .../lib/test_generation/bin/_tool.source      | 32 ++++----
 .../lib/test_generation/bin/_tool.template    | 18 ++---
 framework/lib/test_generation/bin/evosuite.sh | 12 +--
 framework/lib/test_generation/bin/randoop.sh  |  2 +
 .../compile-errors/test-111-112.diff          | 13 ++++
 .../compile-errors/test-93-97.diff            | 13 ++++
 .../compile-errors/test-99-109.diff           | 13 ++++
 .../Mockito/chooseDepedencyVersion.sh         |  6 +-
 .../projects/Mockito/setMutationCompiler.sh   | 12 +--
 framework/test/get_klocs.sh                   | 15 ++--
 framework/test/test.include                   |  3 +-
 framework/test/test_bug_mining.sh             | 77 +++++++++----------
 framework/test/test_cp.sh                     | 14 ++--
 framework/test/test_d4j_query.sh              | 34 ++++----
 framework/test/test_export_command.sh         | 29 ++++---
 framework/test/test_fix_test_suite.sh         | 15 ++--
 framework/test/test_gen_tests.sh              | 36 ++++-----
 framework/test/test_mutation_analysis.sh      |  8 +-
 framework/test/test_style.sh                  | 22 ++++++
 framework/test/test_tutorial.sh               | 10 +--
 framework/test/test_verify_bugs.sh            | 29 ++++---
 init.sh                                       |  4 +-
 23 files changed, 247 insertions(+), 173 deletions(-)
 mode change 100644 => 100755 framework/lib/test_generation/bin/_tool.template
 create mode 100644 framework/projects/JacksonDatabind/compile-errors/test-111-112.diff
 create mode 100644 framework/projects/JacksonDatabind/compile-errors/test-93-97.diff
 create mode 100644 framework/projects/JacksonDatabind/compile-errors/test-99-109.diff
 create mode 100755 framework/test/test_style.sh

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8f9e5e6e2..8b42759e4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -62,6 +62,9 @@ jobs:
     - run: carton exec ./test_bug_mining.sh
       name: test_bug_mining.sh
       working-directory: "./framework/test"
+    - run: carton exec ./test_style.sh
+      name: test_style.sh
+      working-directory: "./framework/test"
 
     # Verify a few select bugs to detect serious breakages early.
     - run: carton exec ./test_verify_bugs.sh -p Collections -b 10 -A
diff --git a/framework/lib/test_generation/bin/_tool.source b/framework/lib/test_generation/bin/_tool.source
index bd8d36fe5..991ac7f3c 100755
--- a/framework/lib/test_generation/bin/_tool.source
+++ b/framework/lib/test_generation/bin/_tool.source
@@ -1,3 +1,4 @@
+#!/bin/bash
 #
 # This file provides helper functions for the wrapper shell scripts of the test
 # generation tools. This file should be included in each wrapper shell script:
@@ -22,7 +23,8 @@ die() {
 # Check whether an environment variable is set -- if not, die with an error message
 check_env() {
     local var="$1"
-    local val=$(eval echo \$$var)
+    local val
+    val="$(eval echo \$$var)"
     [ -z "$val" ] && die "Variable $var not set!"
 }
 
@@ -30,48 +32,48 @@ check_env() {
 # source file of the provided class name.
 get_rel_src_path() {
     local class="$1"
-    local src_dir=$($D4J_HOME/framework/bin/defects4j \
-            export -p dir.src.classes -w $D4J_DIR_WORKDIR 2> /dev/null)
-    echo "$src_dir/$(echo $class | tr '.' '/').java"
+    local src_dir; src_dir=$("$D4J_HOME"/framework/bin/defects4j \
+            export -p dir.src.classes -w "$D4J_DIR_WORKDIR" 2> /dev/null)
+    echo "$src_dir/$(echo "$class" | tr '.' '/').java"
 }
 
 # Get the absolute path to the source file of the provided class name.
 get_abs_src_path() {
     local class="$1"
-    echo "$D4J_DIR_WORKDIR/$(get_rel_src_path $class)"
+    echo "$D4J_DIR_WORKDIR/$(get_rel_src_path "$class")"
 }
 
 # Get the project classpath -- that is, the classpath to compile and run the
 # checked-out Defects4J project version.
 get_project_cp() {
-    $D4J_HOME/framework/bin/defects4j \
-            export -p cp.compile -w $D4J_DIR_WORKDIR 2> /dev/null
+    "$D4J_HOME"/framework/bin/defects4j \
+            export -p cp.compile -w "$D4J_DIR_WORKDIR" 2> /dev/null
 }
 
 # Parse a tool's config file: ignore comments and replace newlines with spaces.
 parse_config() {
     local file=$1
-    grep -v "\s*#" $file | tr '\n' ' '
+    grep -v "\s*#" "$file" | tr '\n' ' '
 }
 
 # Returns the list of all classes for the current bug
 get_all_classes() {
-    local src_dir=$($D4J_HOME/framework/bin/defects4j \
-            export -p dir.src.classes -w $D4J_DIR_WORKDIR 2> /dev/null)
-    (cd $D4J_DIR_WORKDIR/$src_dir && \
+    local src_dir; src_dir=$("$D4J_HOME"/framework/bin/defects4j \
+            export -p dir.src.classes -w "$D4J_DIR_WORKDIR" 2> /dev/null)
+    (cd "$D4J_DIR_WORKDIR/$src_dir" && \
             find . -name "*.java" | tr '/' '.' | sed -e 's/^\.*//g' | sed -e 's/\.java//g')
 }
 
 # Returns the list of all relevant classes for the current bug
 get_relevant_classes() {
-    $D4J_HOME/framework/bin/defects4j \
-            export -p classes.relevant -w $D4J_DIR_WORKDIR 2> /dev/null
+    "$D4J_HOME"/framework/bin/defects4j \
+            export -p classes.relevant -w "$D4J_DIR_WORKDIR" 2> /dev/null
 }
 
 # Returns the list of all modified classes for the current bug
 get_modified_classes() {
-    $D4J_HOME/framework/bin/defects4j \
-            export -p classes.modified -w $D4J_DIR_WORKDIR 2> /dev/null
+    "$D4J_HOME"/framework/bin/defects4j \
+            export -p classes.modified -w "$D4J_DIR_WORKDIR" 2> /dev/null
 }
 
 # Output a command, execute it, and print whether it succeeded or failed.
diff --git a/framework/lib/test_generation/bin/_tool.template b/framework/lib/test_generation/bin/_tool.template
old mode 100644
new mode 100755
index 7e86d3218..7be46cf81
--- a/framework/lib/test_generation/bin/_tool.template
+++ b/framework/lib/test_generation/bin/_tool.template
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 #
 # Wrapper script for <generator name>
 #
@@ -26,25 +26,25 @@ if [ -z "$D4J_DIR_TESTGEN_BIN" ]; then
 fi
 
 # General helper functions
-source $D4J_DIR_TESTGEN_BIN/_tool.source
+source "$D4J_DIR_TESTGEN_BIN"/_tool.source
 
 # The classpath to compile and run the project
-project_cp=$(get_project_cp)
+project_cp="$(get_project_cp)"
 
 # Read all additional configuration parameters
-add_config=$(parse_config $D4J_DIR_TESTGEN_BIN/<generator id>.config)
+add_config=$(parse_config "$D4J_DIR_TESTGEN_BIN"/<generator id>.config)
 
 # Make sure the provided test mode is supported
-if [ $D4J_TEST_MODE == "regression" ]; then
-    ...
-elif [ $D4J_TEST_MODE == "error-revealing" ]; then
-    ...
+if [ "$D4J_TEST_MODE" = "regression" ]; then
+    : # TODO ...
+elif [ "$D4J_TEST_MODE" = "error-revealing" ]; then
+    : # TODO ...
 else
     die "Unsupported test mode: $D4J_TEST_MODE"
 fi
 
 # The command that invokes the test generator
-cmd="... $add_config"
+cmd="... $add_config ... $project_cp ..."
 
 # Run the test-generation command
 if ! exec_cmd "$cmd"; then
diff --git a/framework/lib/test_generation/bin/evosuite.sh b/framework/lib/test_generation/bin/evosuite.sh
index e44d3b048..3a1a3fafc 100755
--- a/framework/lib/test_generation/bin/evosuite.sh
+++ b/framework/lib/test_generation/bin/evosuite.sh
@@ -26,16 +26,16 @@ if [ -z "$D4J_DIR_TESTGEN_BIN" ]; then
 fi
 
 # General helper functions
-source $D4J_DIR_TESTGEN_BIN/_tool.source
+source "$D4J_DIR_TESTGEN_BIN"/_tool.source
 
 # The classpath to compile and run the project
 project_cp=$(get_project_cp)
 
 # Read all additional configuration parameters
-add_config=$(parse_config $D4J_DIR_TESTGEN_BIN/evosuite.config)
+add_config=$(parse_config "$D4J_DIR_TESTGEN_BIN"/evosuite.config)
 
 # Make sure the provided test mode is supported
-if [ $D4J_TEST_MODE != "regression" ]; then
+if [ "$D4J_TEST_MODE" != "regression" ]; then
     die "Unsupported test mode: $D4J_TEST_MODE"
 fi
 
@@ -47,10 +47,12 @@ if [[ $(tail -c1 "$D4J_FILE_TARGET_CLASSES" | wc -l) -eq 0 ]]; then
 fi
 
 # Compute the budget per target class; evenly split the time for search and assertions
-num_classes=$(cat $D4J_FILE_TARGET_CLASSES | wc -l)
+num_classes=$(wc -l < "$D4J_FILE_TARGET_CLASSES")
 budget=$(echo "$D4J_TOTAL_BUDGET/2/$num_classes" | bc)
 
-for class in $(cat $D4J_FILE_TARGET_CLASSES); do
+# shellcheck disable=SC2013 # reading words rather than lines, I suppose
+for class in $(cat "$D4J_FILE_TARGET_CLASSES"); do
+    #shellcheck disable=SC2153 # D4J_DIR_TESTGEN_LIB is not a typo of D4J_DIR_TESTGEN_BIN
     cmd="java -cp $D4J_DIR_TESTGEN_LIB/evosuite-current.jar org.evosuite.EvoSuite \
     -class $class \
     -projectCP $project_cp \
diff --git a/framework/lib/test_generation/bin/randoop.sh b/framework/lib/test_generation/bin/randoop.sh
index e296e477d..e5562199b 100755
--- a/framework/lib/test_generation/bin/randoop.sh
+++ b/framework/lib/test_generation/bin/randoop.sh
@@ -62,8 +62,10 @@ REG_BASE_NAME=RegressionTest
 ERR_BASE_NAME=ErrorTest
 
 # Print Randoop version
+#shellcheck disable=SC2153 # D4J_DIR_TESTGEN_LIB is not a typo of D4J_DIR_TESTGEN_BIN
 version=$(java -cp "$D4J_DIR_TESTGEN_LIB/randoop-current.jar" randoop.main.Main | head -1)
 printf "\n(%s)" "$version" >&2
+# shellcheck disable=SC1083
 printf ".%.0s" {1..expr 73 - length "$version"} >&2
 printf " " >&2
 
diff --git a/framework/projects/JacksonDatabind/compile-errors/test-111-112.diff b/framework/projects/JacksonDatabind/compile-errors/test-111-112.diff
new file mode 100644
index 000000000..f35630aa9
--- /dev/null
+++ b/framework/projects/JacksonDatabind/compile-errors/test-111-112.diff
@@ -0,0 +1,13 @@
+diff --git a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+index f7d1517ed..0fc5e357d 100644
+--- a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
++++ b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+@@ -80,7 +80,7 @@ public class IllegalTypesCheckTest extends BaseMapTest
+     public void testJDKTypes1855() throws Exception
+     {
+         // apparently included by JDK?
+-        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
++//        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
+ 
+         // also: we can try some form of testing, even if bit contrived...
+         _testIllegalType(BogusPointcutAdvisor.class);
diff --git a/framework/projects/JacksonDatabind/compile-errors/test-93-97.diff b/framework/projects/JacksonDatabind/compile-errors/test-93-97.diff
new file mode 100644
index 000000000..f35630aa9
--- /dev/null
+++ b/framework/projects/JacksonDatabind/compile-errors/test-93-97.diff
@@ -0,0 +1,13 @@
+diff --git a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+index f7d1517ed..0fc5e357d 100644
+--- a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
++++ b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+@@ -80,7 +80,7 @@ public class IllegalTypesCheckTest extends BaseMapTest
+     public void testJDKTypes1855() throws Exception
+     {
+         // apparently included by JDK?
+-        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
++//        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
+ 
+         // also: we can try some form of testing, even if bit contrived...
+         _testIllegalType(BogusPointcutAdvisor.class);
diff --git a/framework/projects/JacksonDatabind/compile-errors/test-99-109.diff b/framework/projects/JacksonDatabind/compile-errors/test-99-109.diff
new file mode 100644
index 000000000..f35630aa9
--- /dev/null
+++ b/framework/projects/JacksonDatabind/compile-errors/test-99-109.diff
@@ -0,0 +1,13 @@
+diff --git a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+index f7d1517ed..0fc5e357d 100644
+--- a/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
++++ b/src/test/java/com/fasterxml/jackson/databind/interop/IllegalTypesCheckTest.java
+@@ -80,7 +80,7 @@ public class IllegalTypesCheckTest extends BaseMapTest
+     public void testJDKTypes1855() throws Exception
+     {
+         // apparently included by JDK?
+-        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
++//        _testIllegalType("com.sun.org.apache.bcel.internal.util.ClassLoader");
+ 
+         // also: we can try some form of testing, even if bit contrived...
+         _testIllegalType(BogusPointcutAdvisor.class);
diff --git a/framework/projects/Mockito/chooseDepedencyVersion.sh b/framework/projects/Mockito/chooseDepedencyVersion.sh
index 6df30386f..490f70bb2 100755
--- a/framework/projects/Mockito/chooseDepedencyVersion.sh
+++ b/framework/projects/Mockito/chooseDepedencyVersion.sh
@@ -4,10 +4,10 @@
 # $1 = workDir
 # $2 = D4J_HOME
 
-cd $1
+cd "$1" || (echo "cannot cd to workdir $1" && exit 1)
 ./gradlew dependencies >> tmpDepend.txt
 if grep -q buddy tmpDepend.txt; then
-    version=`cat tmpDepend.txt | grep buddy | cut -d: -f 3 | head -1`
-    cp $2/framework/projects/Mockito/byte-buddy/byte-buddy-$version.jar $1/compileLib/
+    version=$(grep buddy tmpDepend.txt | head -1 | cut -d: -f 3)
+    cp "$2/framework/projects/Mockito/byte-buddy/byte-buddy-$version.jar" "$1/compileLib/"
 fi
 rm tmpDepend.txt
diff --git a/framework/projects/Mockito/setMutationCompiler.sh b/framework/projects/Mockito/setMutationCompiler.sh
index 1073c1fe1..f598b9810 100755
--- a/framework/projects/Mockito/setMutationCompiler.sh
+++ b/framework/projects/Mockito/setMutationCompiler.sh
@@ -2,11 +2,13 @@
 # $1 = working directory
 # $2 = location of Defects4J (D4J_HOME)
 
-WORK_DIR=$1
-D4J_HOME=$2
+WORK_DIR="$1"
+D4J_HOME="$2"
 
 BUILD_FILE="build.gradle"
 
-echo >> $WORK_DIR/$BUILD_FILE
-echo "compileJava.options.fork = true" >> $WORK_DIR/$BUILD_FILE
-echo "compileJava.options.forkOptions.executable = '$D4J_HOME/major/bin/major'" >> $WORK_DIR/$BUILD_FILE
+{
+    echo;
+    echo "compileJava.options.fork = true";
+    echo "compileJava.options.forkOptions.executable = '$D4J_HOME/major/bin/major'";
+} >> "$WORK_DIR/$BUILD_FILE"
diff --git a/framework/test/get_klocs.sh b/framework/test/get_klocs.sh
index 4f50cf5af..431546ecc 100755
--- a/framework/test/get_klocs.sh
+++ b/framework/test/get_klocs.sh
@@ -8,8 +8,9 @@
 ################################################################################
 
 # Must use Java version 8.
-JAVA_VERSION_STRING=`java -version 2>&1 | head -1`
-JAVA_RELEASE_NUMBER=`echo $JAVA_VERSION_STRING | sed 's/^.*1\.\(.\).*/\1/'`
+JAVA_VERSION_STRING=$(java -version 2>&1 | head -1)
+# shellcheck disable=SC2001 # variable substitution does not suffice; needs sed.
+JAVA_RELEASE_NUMBER=$(echo "$JAVA_VERSION_STRING" | sed 's/^.*1\.\(.\).*/\1/')
 if [[ "$JAVA_RELEASE_NUMBER" != "8" ]]; then
  echo Must use Java version 8
  exit
@@ -37,18 +38,20 @@ if [ -z "$1" ] ; then
     bids=( 1 2 3 4 5 )
 else
 # Generate tests for supplied project list
+    # shellcheck disable=SC2206
     projects=( $1 )
     if [ -z "$2" ] ; then
 # Generate tests for all bids
         bids=( 1 2 3 4 5 )
     else
 # Generate tests for supplied bid list
+        # shellcheck disable=SC2206
         bids=( $2 )
     fi
 fi
 
-echo "Projects: ${projects[@]}"
-echo "Bug ids: ${bids[@]}"
+echo "Projects: " "${projects[@]}"
+echo "Bug ids: " "${bids[@]}"
 
 # We want the 'fixed' version of the sample.
 type=f
@@ -57,9 +60,9 @@ for pid in "${projects[@]}"; do
     for bid in "${bids[@]}"; do
         vid=${bid}$type
 
-        run_klocs.pl -p $pid -v $vid -n 1 -o $randoop_dir || die "run klocs on $pid-$vid"
+        run_klocs.pl -p "$pid" -v "$vid" -n 1 -o "$randoop_dir" || die "run klocs on $pid-$vid"
     done
 done
 
 # delete tmp file directory
-rm -rf $randoop_dir
+rm -rf "$randoop_dir"
diff --git a/framework/test/test.include b/framework/test/test.include
index 5dcc15e32..8a573058a 100755
--- a/framework/test/test.include
+++ b/framework/test/test.include
@@ -65,7 +65,8 @@ print_result() {
     printf "\n$text\n" 1>&2
 }
 
-# Print and log error message, and terminate script if HALT_ON_ERROR is set
+# Print and log error message, and set ERROR.
+# Terminate script if HALT_ON_ERROR is set.
 # die <error_text>
 die() {
     echo "Error: $1" 1>&2
diff --git a/framework/test/test_bug_mining.sh b/framework/test/test_bug_mining.sh
index 8daa6df98..bfe68a795 100755
--- a/framework/test/test_bug_mining.sh
+++ b/framework/test/test_bug_mining.sh
@@ -7,7 +7,7 @@
 
 set -e
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -31,8 +31,7 @@ _check_output() {
     sort "$actual" > "$actual.sorted"
     sort "$expected" > "$expected.sorted"
 
-    cmp --silent "$expected.sorted" "$actual.sorted"
-    if [ $? -ne 0 ]; then
+    if ! cmp --silent "$expected.sorted" "$actual.sorted" ; then
         rm -f "$actual.sorted" "$expected.sorted"
         die "'$actual' is not equal to '$expected'!"
     fi
@@ -49,11 +48,11 @@ fi
 # remote resource is newer.  Works around connections that hang.  Takes a
 # single command-line argument, a URL.
 download_url() {
-    BASENAME=`basename ${@: -1}`
+    BASENAME=$(basename "${@: -1}")
     if [ "$(uname)" = "Darwin" ] ; then
         wget -nv -N "$@"
     else
-	timeout 300 curl -s -S -R -L -O -z "$BASENAME" "$@" || (echo "retrying curl $@" && rm -f "$BASENAME" && curl -R -L -O -z "$BASENAME" "$@")
+	timeout 300 curl -s -S -R -L -O -z "$BASENAME" "$@" || (echo "retrying curl $*" && rm -f "$BASENAME" && curl -R -L -O -z "$BASENAME" "$@")
     fi
 }
 
@@ -69,8 +68,8 @@ test_create_project() {
     local repository_url="$4"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./create-project.pl -p $project_id -n $project_name -w $work_dir -r $repository_url || die "Create project script has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./create-project.pl -p "$project_id" -n "$project_name" -w "$work_dir" -r "$repository_url" || die "Create project script has failed"
     popd > /dev/null 2>&1
 
     # Check whether expected directories exist
@@ -114,8 +113,8 @@ test_download_issues() {
     local issues_file="$work_dir/issues.txt"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./download-issues.pl -g $issue_tracker_name -t $issue_tracker_project_id -o $issues_dir -f $issues_file || die "Download of all issues from the issue tracker has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./download-issues.pl -g "$issue_tracker_name" -t "$issue_tracker_project_id" -o "$issues_dir" -f "$issues_file" || die "Download of all issues from the issue tracker has failed"
     popd > /dev/null 2>&1
 
     # Check whether expected files exist
@@ -138,11 +137,11 @@ test_crossref_commmit_issue() {
     local issues_file="$work_dir/issues.txt"
     local commit_db_file="$work_dir/framework/projects/$project_id/$BUGS_CSV_ACTIVE"
 
-    git --git-dir=$repository_dir log --reverse > $git_log_file || die "Git log has failed"
+    git --git-dir="$repository_dir" log --reverse > "$git_log_file" || die "Git log has failed"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./vcs-log-xref.pl -e $regex -l $git_log_file -r $repository_dir -i $issues_file -f $commit_db_file || die "Crossreference of commits and issues ids has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./vcs-log-xref.pl -e "$regex" -l "$git_log_file" -r "$repository_dir" -i "$issues_file" -f "$commit_db_file" || die "Crossreference of commits and issues ids has failed"
     popd > /dev/null 2>&1
 
     # Check whether expected files exist
@@ -171,16 +170,16 @@ test_initialize_revisions() {
     mkdir -p "$lib_dir"
 
     mkdir -p "$lib_dir/junit/junit/4.12"
-    (cd "$lib_dir/junit/junit/4.12" && download_url https://repo1.maven.org/maven2/junit/junit/4.12/junit-4.12.jar || die "Failed to download junit-4.12.jar")
+    (cd "$lib_dir/junit/junit/4.12" && download_url https://repo1.maven.org/maven2/junit/junit/4.12/junit-4.12.jar) || die "Failed to download junit-4.12.jar"
     mkdir -p "$lib_dir/org/apache/commons/commons-lang3/3.4"
-    (cd "$lib_dir/org/apache/commons/commons-lang3/3.4" && download_url https://repo1.maven.org/maven2/org/apache/commons/commons-lang3/3.4/commons-lang3-3.4.jar || die "Failed to download commons-lang3-3.4.jar")
+    (cd "$lib_dir/org/apache/commons/commons-lang3/3.4" && download_url https://repo1.maven.org/maven2/org/apache/commons/commons-lang3/3.4/commons-lang3-3.4.jar) || die "Failed to download commons-lang3-3.4.jar"
     mkdir -p "$lib_dir/org/hamcrest/hamcrest-core/1.3"
-    (cd "$lib_dir/org/hamcrest/hamcrest-core/1.3" && download_url https://repo1.maven.org/maven2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar || die "Failed to download hamcrest-core-1.3.jar")
+    (cd "$lib_dir/org/hamcrest/hamcrest-core/1.3" && download_url https://repo1.maven.org/maven2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar) || die "Failed to download hamcrest-core-1.3.jar"
     # End of fix for Java-7
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./initialize-revisions.pl -p $project_id -w $work_dir -b $bug_id || die "Initialize revisions script has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./initialize-revisions.pl -p "$project_id" -w "$work_dir" -b "$bug_id" || die "Initialize revisions script has failed"
     popd > /dev/null 2>&1
 
     local analyzer_output_dir="framework/projects/$project_id/analyzer_output/$bug_id"
@@ -191,10 +190,10 @@ test_initialize_revisions() {
     _check_output "$work_dir/$analyzer_output_dir/info" "$RESOURCES_OUTPUT_DIR/$analyzer_output_dir/info"
 
     local commit_db_file="$work_dir/framework/projects/$project_id/$BUGS_CSV_ACTIVE"
-    local rev_v1=$(grep "^$bug_id," "$commit_db_file" | cut -f2 -d',')
-    local rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
-    local rev_v1_build_dir="$work_dir/framework/projects/$project_id/build_files/$rev_v1"
-    local rev_v2_build_dir="$work_dir/framework/projects/$project_id/build_files/$rev_v2"
+    local rev_v1; rev_v1=$(grep "^$bug_id," "$commit_db_file" | cut -f2 -d',')
+    local rev_v2; rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
+    local rev_v1_build_dir; rev_v1_build_dir="$work_dir/framework/projects/$project_id/build_files/$rev_v1"
+    local rev_v2_build_dir; rev_v2_build_dir="$work_dir/framework/projects/$project_id/build_files/$rev_v2"
     [ -s "$rev_v1_build_dir/build.xml" ] || die "$rev_v1_build_dir/build.xml does not exist or it is empty"
     [ -s "$rev_v1_build_dir/maven-build.properties" ] || die "$rev_v1_build_dir/maven-build.properties does not exist or it is empty"
     [ -s "$rev_v1_build_dir/maven-build.xml" ] || die "$rev_v1_build_dir/maven-build.xml does not exist or it is empty"
@@ -224,18 +223,18 @@ test_analyze_project() {
     local bug_id="$5"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./analyze-project.pl -p $project_id -w $work_dir -g $issue_tracker_name -t $issue_tracker_project_id -b $bug_id || die "Analyze project script has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./analyze-project.pl -p "$project_id" -w "$work_dir" -g "$issue_tracker_name" -t "$issue_tracker_project_id" -b "$bug_id" || die "Analyze project script has failed"
     popd > /dev/null 2>&1
 
     local commit_db_file="$work_dir/framework/projects/$project_id/$BUGS_CSV_ACTIVE"
-    local rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
+    local rev_v2; rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
     local failing_tests="framework/projects/$project_id/failing_tests/$rev_v2"
     [ -s "$work_dir/$failing_tests" ] || die "No failing test cases has been reported"
 
     # Same number of failing tests
-    local actual_num_failing_tests=$(grep -a "^--- " "$work_dir/$failing_tests" | wc -l)
-    local expected_num_failing_tests=$(grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests" | wc -l)
+    local actual_num_failing_tests; actual_num_failing_tests=$(grep -a "^--- " "$work_dir/$failing_tests" | wc -l)
+    local expected_num_failing_tests; expected_num_failing_tests=$(grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests" | wc -l)
     if [ "$actual_num_failing_tests" -ne "$expected_num_failing_tests" ]; then
       echo "Expected failing tests:"
       grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$failing_tests"
@@ -263,16 +262,16 @@ test_get_trigger() {
     local bug_id="$3"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./get-trigger.pl -p $project_id -w $work_dir -b $bug_id || die "Get list of triggering test cases has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./get-trigger.pl -p "$project_id" -w "$work_dir" -b "$bug_id" || die "Get list of triggering test cases has failed"
     popd > /dev/null 2>&1
 
     local trigger_tests="framework/projects/$project_id/trigger_tests/$bug_id"
     [ -s "$work_dir/$trigger_tests" ] || die "List of triggering test cases is empty or does not exist"
 
     # Same number of trigger tests
-    local actual_num_trigger_tests=$(grep -a "^--- " "$work_dir/$trigger_tests" | wc -l)
-    local expected_num_trigger_tests=$(grep -a "^--- " "$RESOURCES_OUTPUT_DIR/$trigger_tests" | wc -l)
+    local actual_num_trigger_tests; actual_num_trigger_tests=$(grep -c -a "^--- " "$work_dir/$trigger_tests")
+    local expected_num_trigger_tests; expected_num_trigger_tests=$(grep -c -a "^--- " "$RESOURCES_OUTPUT_DIR/$trigger_tests")
     [ "$actual_num_trigger_tests" -eq "$expected_num_trigger_tests" ] || die "Expected $expected_num_trigger_tests trigger tests and got $actual_num_trigger_tests"
 
     # Same trigger tests
@@ -292,8 +291,8 @@ test_get_metadata() {
     local bug_id="$3"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./get-metadata.pl -p $project_id -w $work_dir -b $bug_id || die "Metadata extraction has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./get-metadata.pl -p "$project_id" -w "$work_dir" -b "$bug_id" || die "Metadata extraction has failed"
     popd > /dev/null 2>&1
 
     local relevant_tests="framework/projects/$project_id/relevant_tests/$bug_id"
@@ -324,8 +323,8 @@ test_promote_to_db() {
     local repository_dir="$work_dir/project_repos/$project_name.git"
 
     pushd . > /dev/null 2>&1
-    cd $BUG_MINING_FRAMEWORK_DIR
-    ./promote-to-db.pl -p $project_id -w $work_dir -r $repository_dir -b $bug_id || die "Promotion of $project_id-$bug_id has failed"
+    cd "$BUG_MINING_FRAMEWORK_DIR"
+    ./promote-to-db.pl -p "$project_id" -w "$work_dir" -r "$repository_dir" -b "$bug_id" || die "Promotion of $project_id-$bug_id has failed"
     popd > /dev/null 2>&1
 
     _check_output "$HERE/../core/Project/$project_id.pm" "$work_dir/framework/core/Project/$project_id.pm"
@@ -333,17 +332,17 @@ test_promote_to_db() {
     [ -d "$HERE/../projects/$project_id" ] || die "Project directory does not exist"
 
     local commit_db_file="$work_dir/framework/projects/$project_id/$BUGS_CSV_ACTIVE"
-    local rev_v1=$(grep "^$bug_id," "$commit_db_file" | cut -f2 -d',')
-    local rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
+    local rev_v1; rev_v1=$(grep "^$bug_id," "$commit_db_file" | cut -f2 -d',')
+    local rev_v2; rev_v2=$(grep "^$bug_id," "$commit_db_file" | cut -f3 -d',')
 
     local failing_tests="projects/$project_id/failing_tests/$rev_v2"
     _check_output "$HERE/../$failing_tests" "$work_dir/framework/$failing_tests"
 
     for dir in "build_files/$rev_v1" "build_files/$rev_v2"; do
         while read -r f; do
-            f_name=$(basename $f)
+            f_name=$(basename "$f")
             _check_output "$HERE/../projects/$project_id/$dir/$f_name" "$f"
-        done < <(find "$(cd $work_dir/framework/projects/$project_id/$dir; pwd)" -type f)
+        done < <(find "$(cd "$work_dir/framework/projects/$project_id/$dir"; pwd)" -type f)
     done
 
     local loaded_classes="projects/$project_id/loaded_classes"
@@ -426,7 +425,7 @@ if [ "$ERROR" -ne "0" ]; then
     printf '=%.s' $(seq 1 80) 1>&2
     echo 1>&2
     echo "The following errors occurred:" 1>&2
-    cat $LOG 1>&2
+    cat "$LOG" 1>&2
 fi
 
 # Indicate whether an error occurred
diff --git a/framework/test/test_cp.sh b/framework/test/test_cp.sh
index f13c9488d..f91c3ae26 100755
--- a/framework/test/test_cp.sh
+++ b/framework/test/test_cp.sh
@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -13,7 +13,7 @@ init
 
 # Print usage message
 usage() {
-    local known_pids=$(defects4j pids)
+    local known_pids; known_pids=$(defects4j pids)
     echo "usage: $0 [-p <project id>]"
     echo "Project ids:"
     for pid in $known_pids; do
@@ -50,21 +50,21 @@ main() {
   echo "Temporary directory: $TMP_ROOT" >"$LOG"
 
   for PID in $PIDS; do
-    for BID in $(defects4j bids -p $PID); do
+    for BID in $(defects4j bids -p "$PID"); do
       DIR="$TMP_ROOT/$PID-$BID"
-      defects4j checkout -p $PID -v${BID}f -w "$DIR"
+      defects4j checkout -p "$PID" -v"${BID}"f -w "$DIR"
       defects4j compile -w "$DIR"
       echo "$PID-$BID: start" >> "$LOG"
       for cp in "cp.compile" "cp.test"; do
         key="$PID-$BID-$cp"
         echo "  - $key: $(defects4j export -p $cp -w "$DIR")" >> "$LOG"
-        check_cp_entries $key $(defects4j export -p $cp -w "$DIR") || ERROR=1
+        check_cp_entries "$key" "$(defects4j export -p $cp -w "$DIR")" || ERROR=1
       done
       echo "$PID-$BID: done" >> "$LOG"
     done
   done
 
-  rm -rf $TMP_ROOT
+  rm -rf "$TMP_ROOT"
 
   exit $ERROR
 }
@@ -73,7 +73,7 @@ main() {
 check_cp_entries() {
   local KEY=$1
   local CP=$2
-  for entry in $(echo $CP | tr ':' '\n'); do
+  for entry in $(echo "$CP" | tr ':' '\n'); do
     [[ -e "$entry" ]] || echo "!!! Invalid CP entry ($KEY): $entry" >> "$LOG"
   done
 }
diff --git a/framework/test/test_d4j_query.sh b/framework/test/test_d4j_query.sh
index 6ed5cdfb5..ccc5d43ac 100755
--- a/framework/test/test_d4j_query.sh
+++ b/framework/test/test_d4j_query.sh
@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -16,39 +16,39 @@ result=`diff $HERE/temp $HERE/resources/output/d4j-query/1`
 
 [ "$result" == "" ] || die "query \"-p Collections\" -H failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
 
-$BASE_DIR/framework/bin/defects4j query -p Collections >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/2`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/2)
 
 [ "$result" == "" ] || die "query \"-p Collections\" failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
 
-$BASE_DIR/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/3`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/3)
 
 [ "$result" == "" ] || die "query \"-p Collections -q \"revision.id.buggy,classes.modified\"\" failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
 
-$BASE_DIR/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" -D >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/4`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" -D >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/4)
 
 [ "$result" == "" ] || die "query \"-p Collections -q \"revision.id.buggy,classes.modified\" -D\" failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
 
-$BASE_DIR/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" -A >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/5`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections -q "revision.id.buggy,classes.modified" -A >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/5)
 
 [ "$result" == "" ] || die "query \"-p Collections -q \"revision.id.buggy,classes.modified\" -A\" failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
 
-$BASE_DIR/framework/bin/defects4j query -p Collections -q "deprecated.reason" -A >> $HERE"/temp"
-result=`diff $HERE/temp $HERE/resources/output/d4j-query/6`
+"$BASE_DIR"/framework/bin/defects4j query -p Collections -q "deprecated.reason" -A >> "$HERE"/temp
+result=$(diff "$HERE"/temp "$HERE"/resources/output/d4j-query/6)
 
 [ "$result" == "" ] || die "query \"-p Collections -q \"deprecated.reason\" -A\" failed: $result"
 
-rm $HERE"/temp"
+rm "$HERE"/temp
diff --git a/framework/test/test_export_command.sh b/framework/test/test_export_command.sh
index b8f4f2103..ab36b358e 100755
--- a/framework/test/test_export_command.sh
+++ b/framework/test/test_export_command.sh
@@ -10,7 +10,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -25,14 +25,12 @@ _run_export_command() {
     local exp_cmp="$2"
     local exp_out=""
 
-    pushd . > /dev/null 2>&1
-    cd "$work_dir"
-        exp_out=$(defects4j export -p "$exp_cmp")
-        if [ $? -ne 0 ]; then
-            popd > /dev/null 2>&1
+    pushd "$work_dir" > /dev/null 2>&1 || (echo "Cannot pushd to $work_dir" && exit 1)
+        if ! defects4j export -p "$exp_cmp" ; then
+            popd > /dev/null 2>&1 || (echo "Cannot popd" && exit 1)
             return 1
         fi
-    popd > /dev/null 2>&1
+    popd > /dev/null 2>&1 || (echo "Cannot popd" && exit 1)
 
     echo "$exp_out"
     return 0
@@ -48,7 +46,8 @@ test_export_properties() {
     #################################################################
     # Iterate over all bugs
     #################################################################
-    local bids="$(get_bug_ids $BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE)"
+    local bids
+    bids="$(get_bug_ids "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE")"
     for bid in $bids; do
         local work_dir="$test_dir/$pid/$bid"
         mkdir -p "$work_dir"
@@ -58,9 +57,8 @@ test_export_properties() {
         #################################################################
         # Check "dir.bin.tests"
         #################################################################
-        local test_classes_dir=""
-        test_classes_dir=$(_run_export_command "$work_dir" "dir.bin.tests")
-        if [ $? -ne 0 ]; then
+        local test_classes_dir=""; 
+        if ! test_classes_dir=$(_run_export_command "$work_dir" "dir.bin.tests") ; then
             die "Export command of $pid-$bid has failed"
         fi
 
@@ -134,8 +132,7 @@ test_export_properties() {
         # Check "dir.bin.classes"
         #################################################################
         local classes_dir=""
-        classes_dir=$(_run_export_command "$work_dir" "dir.bin.classes")
-        if [ $? -ne 0 ]; then
+        if ! classes_dir=$(_run_export_command "$work_dir" "dir.bin.classes") ; then
             die "Export command of $pid-$bid has failed"
         fi
 
@@ -181,7 +178,7 @@ test_export_properties() {
 
 # Print usage message and exit
 usage() {
-    local known_pids=$(defects4j pids)
+    local known_pids; known_pids=$(defects4j pids)
     echo "usage: $0 -p <project id>"
     echo "Project ids:"
     for pid in $known_pids; do
@@ -214,7 +211,7 @@ fi
 for PID in $PIDS; do
     HALT_ON_ERROR=0
     # Run all test cases (and log all results), regardless of whether errors occur
-    test_export_properties $PID || die "Test 'test_export_properties' has failed!"
+    test_export_properties "$PID" || die "Test 'test_export_properties' has failed!"
 done
 
 # Print a summary of what went wrong
@@ -222,7 +219,7 @@ if [ "$ERROR" -ne "0" ]; then
     printf '=%.s' $(seq 1 80) 1>&2
     echo 1>&2
     echo "The following errors occurred:" 1>&2
-    cat $LOG 1>&2
+    cat "$LOG" 1>&2
 fi
 
 # Indicate whether an error occurred
diff --git a/framework/test/test_fix_test_suite.sh b/framework/test/test_fix_test_suite.sh
index adeaff0f9..9960c7a40 100755
--- a/framework/test/test_fix_test_suite.sh
+++ b/framework/test/test_fix_test_suite.sh
@@ -5,7 +5,7 @@
 #
 ################################################################################
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -39,11 +39,11 @@ _check_fix_db() {
 
   [ -s "$fix_db_file" ] || die "Database file 'fix' doesn't exist or is empty!"
 
-  local num_rows=$(cat "$fix_db_file" | wc -l)
+  local num_rows; num_rows=$(wc -l < "$fix_db_file")
   [ "$num_rows" -eq 2 ] || die "Database file 'fix' does not have 2 rows!"
 
   # Convert DOS (\r\n) to Unix (\n) line ending and check data of last row
-  local actual_db_data=$(tr -d '\r' < "$fix_db_file" | tail -n1)
+  local actual_db_data; actual_db_data=$(tr -d '\r' < "$fix_db_file" | tail -n1)
   [ "$actual_db_data" == "$expected_db_data" ] || die "Unexpected result (expected: '$expected_db_data'; actual: '$actual_db_data')!"
 
   return 0
@@ -62,11 +62,12 @@ _create_tar_bz2_file() {
   local suites_dir="$4"
 
   # Create a .tar.bz2 file with all test suites
-  pushd . > /dev/null 2>&1
-  cd "$HERE/resources/input"
+  pushd . > /dev/null 2>&1 || (echo "cannot pushd ." && exit 1)
+  cd "$HERE/resources/input" || (echo "cannot cd to $HERE/resources/input" && exit 1)
     tar_bz2_file="$suites_dir/$pid-$bid-test.0.tar.bz2"
+    # shellcheck disable=SC2086 # $input_files contains multiple files
     tar -jcvf "$tar_bz2_file" $input_files || return 1
-  popd > /dev/null 2>&1
+  popd > /dev/null 2>&1 || (echo "cannot popd" && exit 1)
 
   return 0
 }
@@ -205,6 +206,7 @@ test_MultipleUnitTestsWithMultipleCompilationIssues() {
   local pid="Gson"
   local bid="18f"
 
+  #shellcheck disable=SC2016 # Literal $ in single-quoted string.
   run_fix_test_suite_test_case "$pid" "$bid" \
     'com/google/gson/internal/$Gson$Types_ESTest.java com/google/gson/internal/$Gson$Types_ESTest_scaffolding.java' \
     'com/google/gson/internal/$Gson$Types_ESTest.java com/google/gson/internal/$Gson$Types_ESTest.java.bak com/google/gson/internal/$Gson$Types_ESTest_scaffolding.java' \
@@ -215,6 +217,7 @@ test_MultipleUnitTestsWithMultipleCompilationIssues() {
     return 0
   fi
 
+  #shellcheck disable=SC2016 # Literal $ in single-quoted string.
   run_fix_test_suite_test_case "$pid" "$bid" \
     'com/google/gson/internal/$Gson$Types_ESTest.java com/google/gson/internal/$Gson$Types_ESTest_scaffolding.java' \
     'com/google/gson/internal/$Gson$Types_ESTest.java com/google/gson/internal/$Gson$Types_ESTest.java.bak com/google/gson/internal/$Gson$Types_ESTest_scaffolding.java' \
diff --git a/framework/test/test_gen_tests.sh b/framework/test/test_gen_tests.sh
index ed728da88..1a43e66d1 100755
--- a/framework/test/test_gen_tests.sh
+++ b/framework/test/test_gen_tests.sh
@@ -20,7 +20,7 @@ init
 
 # Print usage message and exit
 usage() {
-    local known_pids=$(defects4j pids)
+    local known_pids; known_pids=$(defects4j pids)
     echo "usage: $0 -p <project id> [-b <bug id> ... | -b <bug id range> ... ]"
     echo "Project ids:"
     for pid in $known_pids; do
@@ -35,7 +35,7 @@ while getopts ":p:b:" opt; do
         p) PID="$OPTARG"
             ;;
         b) if [[ "$OPTARG" =~ ^[0-9]*\.\.[0-9]*$ ]]; then
-                BUGS="$BUGS $(eval echo {$OPTARG})"
+                BUGS="$BUGS $(eval echo "{$OPTARG}")"
            else
                 BUGS="$BUGS $OPTARG"
            fi
@@ -63,12 +63,12 @@ init
 
 # Run all bugs, unless otherwise specified
 if [ "$BUGS" == "" ]; then
-    BUGS="$(get_bug_ids $BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE)"
+    BUGS="$(get_bug_ids "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE")"
 fi
 
 # Create log file
-script_name=$(echo $script | sed 's/\.sh$//')
-LOG="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).log"
+script_name_without_sh=${script//.sh/}
+LOG="$TEST_DIR/${script_name_without_sh}$(printf '_%s_%s' "$PID" $$).log"
 
 ################################################################################
 # Run all generators on the specified bugs, and determine bug detection,
@@ -79,12 +79,12 @@ LOG="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).log"
 HALT_ON_ERROR=0
 
 work_dir="$TMP_DIR/$PID"
-mkdir -p $work_dir
+mkdir -p "$work_dir"
 
 # Clean working directory
-rm -rf "$work_dir/*"
+rm -rf "${work_dir:?}/*"
 
-for bid in $(echo $BUGS); do
+for bid in $BUGS ; do
     # Skip all bug ids that do not exist in the active-bugs csv
     if ! grep -q "^$bid," "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE"; then
         warn "Skipping bug ID that is not listed in active-bugs csv: $PID-$bid"
@@ -95,9 +95,9 @@ for bid in $(echo $BUGS); do
     target_classes="$BASE_DIR/framework/projects/$PID/modified_classes/$bid.src"
 
     # Iterate over all supported generators and generate regression tests
-    for tool in $($BASE_DIR/framework/bin/gen_tests.pl -g help | grep \- | tr -d '-'); do
+    for tool in $("$BASE_DIR"/framework/bin/gen_tests.pl -g help | grep - | tr -d '-'); do
         # Directory for generated test suites
-        suite_src="$tool"
+        # suite_src="$tool"
         suite_num=1
         suite_dir="$work_dir/$tool/$suite_num"
 
@@ -105,28 +105,28 @@ for bid in $(echo $BUGS); do
         vid=${bid}f
 
         # Run generator and the fix script on the generated test suite
-        if ! gen_tests.pl -g "$tool" -p $PID -v $vid -n 1 -o "$TMP_DIR" -b 30 -c "$target_classes"; then
+        if ! gen_tests.pl -g "$tool" -p "$PID" -v "$vid" -n 1 -o "$TMP_DIR" -b 30 -c "$target_classes"; then
             die "run $tool (regression) on $PID-$vid"
             # Skip any remaining analyses (cannot be run), even if halt-on-error is false
             continue
         fi
-        fix_test_suite.pl -p $PID -d "$suite_dir" || die "fix test suite"
+        fix_test_suite.pl -p "$PID" -d "$suite_dir" || die "fix test suite"
 
         # Run test suite and determine bug detection
-        test_bug_detection $PID "$suite_dir"
+        test_bug_detection "$PID" "$suite_dir"
 
         # Run test suite and determine mutation score
-        test_mutation $PID "$suite_dir"
+        test_mutation "$PID" "$suite_dir"
 
         # Run test suite and determine code coverage
-        test_coverage $PID "$suite_dir" 0
+        test_coverage "$PID" "$suite_dir" 0
 
-        rm -rf $work_dir/$tool
+        rm -rf "${work_dir:?}/$tool"
     done
 
     vid=${bid}b
     # Run Randoop to generate error-revealing tests (other tools cannot do so)
-    gen_tests.pl -g randoop -p $PID -v $vid -n 1 -o "$TMP_DIR" -b 30 -c "$target_classes" -E
+    gen_tests.pl -g randoop -p "$PID" -v "$vid" -n 1 -o "$TMP_DIR" -b 30 -c "$target_classes" -E
     # We expect Randoop to not crash; it may or may not create an error-revealing test for this version
     ret=$?
     [ $ret -eq 0 ] || [ $ret -eq 127 ] || die "run $tool (error-revealing) on $PID-$vid"
@@ -139,7 +139,7 @@ if [ $ERROR != 0 ]; then
     printf '=%.s' $(seq 1 80) 1>&2
     echo 1>&2
     echo "The following errors occurred:" 1>&2
-    cat $LOG 1>&2
+    cat "$LOG" 1>&2
 fi
 
 # Indicate whether an error occurred
diff --git a/framework/test/test_mutation_analysis.sh b/framework/test/test_mutation_analysis.sh
index 1b688b277..d2579711c 100755
--- a/framework/test/test_mutation_analysis.sh
+++ b/framework/test/test_mutation_analysis.sh
@@ -7,7 +7,7 @@
 # TODO: There is some code duplication in this test script, which we can avoid
 # by extracting the mutation analysis workflow into a parameterized function. 
 
-HERE=$(cd `dirname $0` && pwd)
+HERE=$(cd "$(dirname "$0")" && pwd) || (echo "cannot cd to $(dirname "$0")" && exit 1)
 
 # Import helper subroutines and variables, and init Defects4J
 source "$HERE/test.include" || exit 1
@@ -51,7 +51,7 @@ _check_mutation_result() {
 
     # The last row of 'summary.csv' does not have an end of line character.
     # Otherwise, using wc would be more intuitive.
-    local num_rows=$(grep -c "^" "$summary_file")
+    local num_rows; num_rows=$(grep -c "^" "$summary_file")
     [ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
 
     # Columns of summary (csv) file:
@@ -143,7 +143,7 @@ _set_vars "Chart" "12f"
 # Remove temporary directory if it already exists
 rm -rf "$pid_vid_dir"
 # Checkout project-version
-defects4j checkout -p $pid -v $vid -w "$pid_vid_dir" || die "It was not possible to checkout $pid-$vid to '$pid_vid_dir'!"
+defects4j checkout -p "$pid" -v "$vid" -w "$pid_vid_dir" || die "It was not possible to checkout $pid-$vid to '$pid_vid_dir'!"
 # Remove the summary file to ensure it is regenerated
 rm -f "$summary_file"
 defects4j mutation -w "$pid_vid_dir" -r || die "Mutation analysis (including all mutants) failed!"
@@ -156,7 +156,7 @@ _set_vars "Mockito" "12f"
 # Remove temporary directory if it already exists
 rm -rf "$pid_vid_dir"
 # Checkout project-version
-defects4j checkout -p $pid -v $vid -w "$pid_vid_dir" || die "It was not possible to checkout $pid-$vid to '$pid_vid_dir'!"
+defects4j checkout -p "$pid" -v "$vid" -w "$pid_vid_dir" || die "It was not possible to checkout $pid-$vid to '$pid_vid_dir'!"
 # Remove the summary file to ensure it is regenerated
 rm -f "$summary_file"
 defects4j mutation -w "$pid_vid_dir" -r || die "Mutation analysis (including all mutants) failed!"
diff --git a/framework/test/test_style.sh b/framework/test/test_style.sh
new file mode 100755
index 000000000..45631b40b
--- /dev/null
+++ b/framework/test/test_style.sh
@@ -0,0 +1,22 @@
+#!/bin/sh
+
+TOPLEVEL="$(git rev-parse --show-toplevel)"
+
+cd "$TOPLEVEL" || (echo "Cannot cd to $TOPLEVEL" && exit 1)
+
+# Check style of sh scripts.
+grep -r -l '^\#! \?\(/bin/\|/usr/bin/env \)sh' --exclude=\*~ "$TOPLEVEL"/framework | while read -r line
+do
+    shellcheck -x -P SCRIPTDIR --format=gcc "$line"
+    checkbashisms "$line"
+done
+
+# Check style of bash scripts.
+grep -r -l '^\#! \?\(/bin/\|/usr/bin/env \)bash' --exclude=\*~ "$TOPLEVEL"/framework | while read -r line
+do
+    shellcheck -x -P SCRIPTDIR --format=gcc "$line"
+done
+for file in "$TOPLEVEL"/init.sh "$TOPLEVEL"/framework/lib/test_generation/bin/_tool.source ; do
+    shellcheck -x -P SCRIPTDIR --format=gcc "$file"
+done
+
diff --git a/framework/test/test_tutorial.sh b/framework/test/test_tutorial.sh
index dd071fd68..06fa6fb49 100755
--- a/framework/test/test_tutorial.sh
+++ b/framework/test/test_tutorial.sh
@@ -23,15 +23,15 @@ vid=${bid}b
 work_dir=$TMP_DIR/$pid-$vid
 
 # Checkout buggy version
-defects4j checkout -p $pid -v $vid -w $work_dir || die "checkout program version $pid-$vid"
+defects4j checkout -p $pid -v $vid -w "$work_dir" || die "checkout program version $pid-$vid"
 
 # Verify that defects4j's config file exists 
-[ -e $work_dir/.defects4j.config ] || die "read config file"
+[ -e "$work_dir"/.defects4j.config ] || die "read config file"
 # Verify that defects4j's config file provides the correct data
-grep -q "pid=$pid" $work_dir/.defects4j.config || die "verify pid in config file"
-grep -q "vid=$vid" $work_dir/.defects4j.config || die "verify vid in config file"
+grep -q "pid=$pid" "$work_dir"/.defects4j.config || die "verify pid in config file"
+grep -q "vid=$vid" "$work_dir"/.defects4j.config || die "verify vid in config file"
 
-cd $work_dir
+cd "$work_dir" || (echo "cannot cd to $work_dir" && exit 1)
 
 # Compile buggy version
 defects4j compile || die "compile program version $pid-$vid"
diff --git a/framework/test/test_verify_bugs.sh b/framework/test/test_verify_bugs.sh
index e7faa081b..65e94946f 100755
--- a/framework/test/test_verify_bugs.sh
+++ b/framework/test/test_verify_bugs.sh
@@ -49,7 +49,7 @@ while getopts ":p:b:AD" opt; do
         p) PID="$OPTARG"
             ;;
         b) if [[ "$OPTARG" =~ ^[0-9]*\.\.[0-9]*$ ]]; then
-                BUGS="$BUGS $(eval echo {$OPTARG})"
+                BUGS="$BUGS $(eval echo "{$OPTARG}")"
            else
                 BUGS="$BUGS $OPTARG"
            fi
@@ -75,7 +75,7 @@ fi
 
 # Run all bugs, unless otherwise specified
 if [ "$BUGS" == "" ]; then
-    BUGS="$(get_bug_ids $BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE)"
+    BUGS="$(get_bug_ids "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE")"
 fi
 
 if [ "$DEBUG" == "-D" ]; then
@@ -83,9 +83,9 @@ if [ "$DEBUG" == "-D" ]; then
 fi
 
 # Create log file
-script_name=$(echo $script | sed 's/\.sh$//')
-LOG="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).log"
-DIR_FAILING="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).failing_tests"
+script_name_without_sh=${script//.sh/}
+LOG="$TEST_DIR/${script_name_without_sh}$(printf '_%s_%s' "$PID" $$).log"
+DIR_FAILING="$TEST_DIR/${script_name_without_sh}$(printf '_%s_%s' "$PID" $$).failing_tests"
 
 ################################################################################
 # Run developer-written tests on all buggy and fixed program versions, and 
@@ -96,15 +96,15 @@ DIR_FAILING="$TEST_DIR/${script_name}$(printf '_%s_%s' $PID $$).failing_tests"
 HALT_ON_ERROR=0
 
 test_dir="$TMP_DIR/test_trigger"
-mkdir -p $test_dir
+mkdir -p "$test_dir"
 
-mkdir -p $DIR_FAILING
+mkdir -p "$DIR_FAILING"
 
 work_dir="$test_dir/$PID"
 
 # Clean working directory
-rm -rf $work_dir
-for bid in $(echo $BUGS); do
+rm -rf "$work_dir"
+for bid in $BUGS ; do
     # Skip all bug ids that do not exist in the active-bugs csv
     if ! grep -q "^$bid," "$BASE_DIR/framework/projects/$PID/$BUGS_CSV_ACTIVE"; then
         warn "Skipping bug ID that is not listed in active-bugs csv: $PID-$bid"
@@ -113,8 +113,7 @@ for bid in $(echo $BUGS); do
 
     for v in "b" "f"; do
         vid=${bid}$v
-        defects4j checkout -p $PID -v "$vid" -w "$work_dir" || die "checkout: $PID-$vid"
-
+        defects4j checkout -p "$PID" -v "$vid" -w "$work_dir" || die "checkout: $PID-$vid"
         defects4j compile -w "$work_dir" || die "compile: $PID-$vid"
         defects4j test $TEST_FLAG -w "$work_dir" || die "run relevant tests: $PID-$vid"
 
@@ -123,7 +122,7 @@ for bid in $(echo $BUGS); do
         triggers=$(num_triggers "$work_dir/failing_tests")
         # Expected number of failing tests for each fixed version is 0!
         if [ $v == "f" ]; then
-            [ $triggers -eq 0 ] \
+            [ "$triggers" -eq 0 ] \
                     || die "verify number of triggering tests: $PID-$vid (expected: 0, actual: $triggers)"
             continue
         fi
@@ -133,9 +132,9 @@ for bid in $(echo $BUGS); do
         expected=$(num_triggers "$BASE_DIR/framework/projects/$PID/trigger_tests/$bid")
 
         # Fail if there are no trigger tests
-        [ $expected -gt 0 ] || die "Metadata error: There are no trigger tests for $PID-$vid"
+        [ "$expected" -gt 0 ] || die "Metadata error: There are no trigger tests for $PID-$vid"
 
-        [ $triggers -eq $expected ] \
+        [ "$triggers" -eq "$expected" ] \
                 || die "verify number of triggering tests: $PID-$vid (expected: $expected, actual: $triggers)"
         for t in $(get_triggers "$BASE_DIR/framework/projects/$PID/trigger_tests/$bid"); do
             grep -q "$t" "$work_dir/failing_tests" || die "expected triggering test $t did not fail"
@@ -153,7 +152,7 @@ if [ $ERROR != 0 ]; then
     printf '=%.s' $(seq 1 80) 1>&2
     echo 1>&2
     echo "The following errors occurred:" 1>&2
-    cat $LOG 1>&2
+    cat "$LOG" 1>&2
 fi
 
 # Indicate whether an error occurred
diff --git a/init.sh b/init.sh
index 8d345458e..cdb7acdde 100755
--- a/init.sh
+++ b/init.sh
@@ -80,7 +80,7 @@ download_url() {
         else
             ZBASENAME=""
         fi
-        (timeout 300 curl -s -S -R -L -O $ZBASENAME "$URL" || (echo "retrying curl $URL" && rm -f "$BASENAME" && curl -R -L -O "$URL")) && echo "Downloaded $URL"
+        (timeout 300 curl -s -S -R -L -O "$ZBASENAME" "$URL" || (echo "retrying curl $URL" && rm -f "$BASENAME" && curl -R -L -O "$URL")) && echo "Downloaded $URL"
     fi
 }
 
@@ -121,7 +121,7 @@ get_modification_timestamp() {
         cmd="stat -f %m $f"
     fi
 
-    local ts=$($cmd)
+    local ts; ts=$($cmd)
     echo "$ts"
 }