diff --git a/scripts/Makefile b/scripts/Makefile
index 03ede47..e548ab1 100644
--- a/scripts/Makefile
+++ b/scripts/Makefile
@@ -1,6 +1,7 @@
 MAKEFILE_DIR := $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
 
 all: \
+    build/checker-framework/checker/dist/checker-qual.jar \
     build/evosuite-1.2.0.jar \
     build/evosuite-standalone-runtime-1.2.0.jar \
     build/hamcrest-core-1.3.jar \
@@ -64,13 +65,21 @@ build/junit-4.12.jar:
 
 build/hamcrest-core-1.3.jar:
 	mkdir -p build
-	cp ../subject-programs/hamcrest-core-1.3.jar build/
+	cp ../subject-programs/jars/hamcrest-core-1.3.jar build/
 
 build/major/bin/ant-replacecall:
 	LATEST_RELEASE=$$(curl -s https://api.github.com/repos/randoop/grt-replacecall/releases/latest | grep -o '"tag_name": "[^"]*' | cut -d'"' -f4) && \
 	wget "https://github.com/randoop/grt-replacecall/releases/download/$${LATEST_RELEASE}/ant-replacecall" && \
 	mv ant-replacecall build/major/bin/
 
+build/checker-framework/checker/dist/checker-qual.jar:
+	mkdir -p build
+	CFVER=3.50.0 && \
+	cd build && wget "https://github.com/typetools/checker-framework/releases/download/checker-framework-$${CFVER}/checker-framework-$${CFVER}.zip" && \
+	unzip -o checker-framework-$${CFVER}.zip && \
+	rm -rf checker-framework && \
+	mv checker-framework-$${CFVER} checker-framework
+
 build/defects4j:
 	mkdir -p build
 	cd build && git clone https://github.com/rjust/defects4j && cd defects4j && cpanm --installdeps . && ./init.sh
diff --git a/scripts/mutation-evosuite.sh b/scripts/mutation-evosuite.sh
index 51e3a71..1ff2ee4 100755
--- a/scripts/mutation-evosuite.sh
+++ b/scripts/mutation-evosuite.sh
@@ -172,7 +172,7 @@ echo
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
 # Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -318,7 +318,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")
diff --git a/scripts/mutation-randoop.sh b/scripts/mutation-randoop.sh
index 9fe7a9d..b9e32bf 100755
--- a/scripts/mutation-randoop.sh
+++ b/scripts/mutation-randoop.sh
@@ -56,12 +56,12 @@ set -o pipefail
 Generator=Randoop
 generator=randoop
 SCRIPT_DIR="$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd -P)"
-SCRIPT_NAME=$(basename -- "$0")
-MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                     # Major home directory, for mutation testing
-RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")     # Randoop jar file
-JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")      # For Bloodhound
-JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")          # For coverage report generation
-REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar") # For replacing undesired method calls
+MAJOR_HOME=$(realpath "${SCRIPT_DIR}/build/major/")                                                # Major home directory, for mutation testing
+RANDOOP_JAR=$(realpath "${SCRIPT_DIR}/build/randoop-all-4.3.4.jar")                                # Randoop jar file
+JACOCO_AGENT_JAR=$(realpath "${SCRIPT_DIR}/build/jacocoagent.jar")                                 # For Bloodhound
+JACOCO_CLI_JAR=$(realpath "${SCRIPT_DIR}/build/jacococli.jar")                                     # For coverage report generation
+REPLACECALL_JAR=$(realpath "${SCRIPT_DIR}/build/replacecall-4.3.4.jar")                            # For replacing undesired method calls
+CHECKER_QUAL_JAR=$(realpath "${SCRIPT_DIR}/build/checker-framework/checker/dist/checker-qual.jar") # For Randoop Impurity
 
 . "$SCRIPT_DIR/defs.sh" # Define shell functions.
 
@@ -70,6 +70,7 @@ require_file "$RANDOOP_JAR"
 require_file "$JACOCO_AGENT_JAR"
 require_file "$JACOCO_CLI_JAR"
 require_file "$REPLACECALL_JAR"
+require_file "$CHECKER_QUAL_JAR"
 
 usejdk8
 JAVA_VER=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}' | awk -F '.' '{sub("^$", "0", $2); print ($1=="1")?$2:$1}')
@@ -219,8 +220,18 @@ echo
 # Path to the base directory of the source code.
 SRC_BASE_DIR="$(realpath "$SCRIPT_DIR/../subject-programs/src/$SUBJECT_PROGRAM")"
 
-# Path to the jar file of the subject program.
-SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/$SUBJECT_PROGRAM.jar")
+if [[ " ${RANDOOP_FEATURES[*]} " =~ " GRT_FUZZING " ]]; then
+  # If randoop features contain "GRT_FUZZING", use annotated subject program jar.
+  ANNOTATED_JAR="$SCRIPT_DIR/../subject-programs/annotated-jars/$SUBJECT_PROGRAM.jar"
+  if [ ! -f "$ANNOTATED_JAR" ]; then
+    echo "${SCRIPT_NAME}: error: GRT_FUZZING enabled but annotated JAR not found: $ANNOTATED_JAR" >&2
+    exit 2
+  fi
+  SRC_JAR=$(realpath "$ANNOTATED_JAR")
+else
+  # Else, use the original subject program jar.
+  SRC_JAR=$(realpath "$SCRIPT_DIR/../subject-programs/jars/$SUBJECT_PROGRAM.jar")
+fi
 
 # Number of classes in given jar file.
 NUM_CLASSES=$(jar -tf "$SRC_JAR" | grep -c '.class')
@@ -353,7 +364,7 @@ case "$SUBJECT_PROGRAM" in
       "$SRC_BASE_DIR/lib/jaxen-core.jar" \
       "$SRC_BASE_DIR/lib/jaxen-jdom.jar" \
       "$SRC_BASE_DIR/lib/saxpath.jar" \
-      "$SCRIPT_DIR/../subject-programs/jaxen-1.1.6.jar"
+      "$SCRIPT_DIR/../subject-programs/jars/jaxen-1.1.6.jar"
     ;;
 
   "joda-time-2.3")
@@ -456,7 +467,7 @@ RANDOOP_BASE_COMMAND=(
   -Xbootclasspath/a:"$JACOCO_AGENT_JAR:$REPLACECALL_JAR"
   -javaagent:"$JACOCO_AGENT_JAR"
   -javaagent:"$REPLACECALL_COMMAND"
-  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR"
+  -classpath "$RANDOOP_CLASSPATH:$RANDOOP_JAR:$CHECKER_QUAL_JAR"
   randoop.main.Main
   gentests
   --testjar="$TARGET_JAR"
diff --git a/subject-programs/annotated-jars/ClassViewer-5.0.5b.jar b/subject-programs/annotated-jars/ClassViewer-5.0.5b.jar
new file mode 100644
index 0000000..62f0506
Binary files /dev/null and b/subject-programs/annotated-jars/ClassViewer-5.0.5b.jar differ
diff --git a/subject-programs/annotated-jars/JSAP-2.1.jar b/subject-programs/annotated-jars/JSAP-2.1.jar
new file mode 100644
index 0000000..4199347
Binary files /dev/null and b/subject-programs/annotated-jars/JSAP-2.1.jar differ
diff --git a/subject-programs/annotated-jars/README.md b/subject-programs/annotated-jars/README.md
new file mode 100644
index 0000000..47f6dc4
--- /dev/null
+++ b/subject-programs/annotated-jars/README.md
@@ -0,0 +1,66 @@
+# Annotated Subject Program JARs
+
+This folder holds subject JARs with purity annotations:  `@Pure`,
+`@SideEffectFree`, `@Impure`, and related qualifiers from
+`org.checkerframework.framework.qual` Compared to `subject-programs/jars/`, the
+compiled bytecode here is the same, but the class files have purity
+annotations. No other code or resources are altered.
+
+The annotations are produced by the Checker Framework whole-program inference.
+
+## Why the annotations matter
+
+The `GRT_FUZZING` feature in `scripts/mutation-randoop.sh` prioritizes impure
+calls to mutate an object's state before exercising additional API entry points.
+The annotations provide the information it needs.
+
+## Rebuilding an annotated JAR
+
+1. **Fetch sources**: Run `scripts/get-all-subject-src.sh` to populate
+   `subject-programs/src/<subject-program>/`.
+2. **Build the plain JAR**: In the subject directory, run the build command
+   found in `subject-programs/README.build`. The result lands in
+   `subject-programs/jars/` or the subject's usual build folder.
+3. **Set up inference tooling**: Point your environment at the local Checker
+   Framework build:
+
+   ```sh
+   export CHECKERFRAMEWORK=/path/to/grt-testing/scripts/build/checker-framework
+   export PATH="$CHECKERFRAMEWORK/annotation-file-utilities/bin:$PATH"
+   export JAVAC_JAR="$CHECKERFRAMEWORK/checker/dist/javac.jar"
+   ```
+
+4. **Set the classpath**: Start with the JAR you just built, then
+   append any dependencies:
+   - Ant projects usually ship extra JARs in a local `jars/` or `lib/` folder.
+   - Maven projects can generate a classpath with
+     `mvn -q dependency:build-classpath -Dmdep.outputFile=target/wpi-classpath.txt`.
+5. **Run inference**: From the subject directory, execute:
+
+   ```sh
+   $CHECKERFRAMEWORK/checker/bin/infer-and-annotate.sh \
+     "org.checkerframework.framework.util.PurityChecker" \
+     "$RUNTIME_CLASSPATH" \
+     $(find src -name "*.java")
+   ```
+
+   The script rewrites the sources in place with the inferred annotations.
+6. **Rebuild**: Repeat the command from step 2 to produce an annotated JAR.
+   Copy it to this folder.
+
+### Worked example (a4j-1.0b)
+
+```sh
+cd subject-programs/src/a4j-1.0b
+ant createJar                              # build the baseline JAR
+export CHECKERFRAMEWORK=...                # reuse the env vars above
+export PATH="$CHECKERFRAMEWORK/annotation-file-utilities/bin:$PATH"
+export JAVAC_JAR="$CHECKERFRAMEWORK/checker/dist/javac.jar"
+RUNTIME_CLASSPATH="../../jars/a4j-1.0b.jar:jars/jox116.jar:jars/log4j-1.2.4.jar"
+$CHECKERFRAMEWORK/checker/bin/infer-and-annotate.sh \
+  "org.checkerframework.framework.util.PurityChecker" \
+  "$RUNTIME_CLASSPATH" \
+  $(find src -name "*.java")
+ant createJar                              # rebuild with annotations
+cp dist/a4j.jar ../../annotated-jars/a4j-1.0b.jar
+```
diff --git a/subject-programs/annotated-jars/a4j-1.0b.jar b/subject-programs/annotated-jars/a4j-1.0b.jar
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rename to subject-programs/jars/ClassViewer-5.0.5b.jar
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similarity index 100%
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rename to subject-programs/jars/JSAP-2.1.jar
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similarity index 100%
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rename to subject-programs/jars/a4j-1.0b.jar
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similarity index 100%
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rename to subject-programs/jars/asm-5.0.1.jar
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similarity index 100%
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rename to subject-programs/jars/bcel-5.2.jar
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similarity index 100%
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rename to subject-programs/jars/commons-cli-1.2.jar
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similarity index 100%
rename from subject-programs/commons-codec-1.9.jar
rename to subject-programs/jars/commons-codec-1.9.jar
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similarity index 100%
rename from subject-programs/commons-collections4-4.0.jar
rename to subject-programs/jars/commons-collections4-4.0.jar
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similarity index 100%
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rename to subject-programs/jars/commons-compress-1.8.jar
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similarity index 100%
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rename to subject-programs/jars/commons-lang3-3.0.jar
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rename to subject-programs/jars/commons-math3-3.2.jar
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similarity index 100%
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rename to subject-programs/jars/commons-primitives-1.0.jar
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rename to subject-programs/jars/dcParseArgs-10.2008.jar
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rename to subject-programs/jars/easymock-3.2.jar
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similarity index 100%
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rename to subject-programs/jars/fixsuite-r48.jar
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similarity index 100%
rename from subject-programs/guava-16.0.1.jar
rename to subject-programs/jars/guava-16.0.1.jar
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similarity index 100%
rename from subject-programs/hamcrest-core-1.3.jar
rename to subject-programs/jars/hamcrest-core-1.3.jar
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similarity index 100%
rename from subject-programs/javassist-3.19.jar
rename to subject-programs/jars/javassist-3.19.jar
diff --git a/subject-programs/javax.mail-1.5.1.jar b/subject-programs/jars/javax.mail-1.5.1.jar
similarity index 100%
rename from subject-programs/javax.mail-1.5.1.jar
rename to subject-programs/jars/javax.mail-1.5.1.jar
diff --git a/subject-programs/jaxen-1.1.6.jar b/subject-programs/jars/jaxen-1.1.6.jar
similarity index 100%
rename from subject-programs/jaxen-1.1.6.jar
rename to subject-programs/jars/jaxen-1.1.6.jar
diff --git a/subject-programs/jcommander-1.35.jar b/subject-programs/jars/jcommander-1.35.jar
similarity index 100%
rename from subject-programs/jcommander-1.35.jar
rename to subject-programs/jars/jcommander-1.35.jar
diff --git a/subject-programs/jdom-1.0.jar b/subject-programs/jars/jdom-1.0.jar
similarity index 100%
rename from subject-programs/jdom-1.0.jar
rename to subject-programs/jars/jdom-1.0.jar
diff --git a/subject-programs/joda-time-2.3.jar b/subject-programs/jars/joda-time-2.3.jar
similarity index 100%
rename from subject-programs/joda-time-2.3.jar
rename to subject-programs/jars/joda-time-2.3.jar
diff --git a/subject-programs/jvc-1.1.jar b/subject-programs/jars/jvc-1.1.jar
similarity index 100%
rename from subject-programs/jvc-1.1.jar
rename to subject-programs/jars/jvc-1.1.jar
diff --git a/subject-programs/nekomud-r16.jar b/subject-programs/jars/nekomud-r16.jar
similarity index 100%
rename from subject-programs/nekomud-r16.jar
rename to subject-programs/jars/nekomud-r16.jar
diff --git a/subject-programs/pmd-core-5.2.2.jar b/subject-programs/jars/pmd-core-5.2.2.jar
similarity index 100%
rename from subject-programs/pmd-core-5.2.2.jar
rename to subject-programs/jars/pmd-core-5.2.2.jar
diff --git a/subject-programs/sat4j-core-2.3.5.jar b/subject-programs/jars/sat4j-core-2.3.5.jar
similarity index 100%
rename from subject-programs/sat4j-core-2.3.5.jar
rename to subject-programs/jars/sat4j-core-2.3.5.jar
diff --git a/subject-programs/shiro-core-1.2.3.jar b/subject-programs/jars/shiro-core-1.2.3.jar
similarity index 100%
rename from subject-programs/shiro-core-1.2.3.jar
rename to subject-programs/jars/shiro-core-1.2.3.jar
diff --git a/subject-programs/slf4j-api-1.7.12.jar b/subject-programs/jars/slf4j-api-1.7.12.jar
similarity index 100%
rename from subject-programs/slf4j-api-1.7.12.jar
rename to subject-programs/jars/slf4j-api-1.7.12.jar
diff --git a/subject-programs/tiny-sql-2.26.jar b/subject-programs/jars/tiny-sql-2.26.jar
similarity index 100%
rename from subject-programs/tiny-sql-2.26.jar
rename to subject-programs/jars/tiny-sql-2.26.jar