Extend java coverage reports to include non-covered files (#9658)

Jacoco is used for code coverage report generation of JVM projects. It
will make use of the dumped class file to generate the report. But only
java classes covered by at least one fuzzer will be included in the
report, other files in the project will be ignored. This PR aims to
point the Jacoco class file discovery folder to the original compiled
project jar file in order to force Jacoco to generate coverage report
with source for all java class of the project.
This came as a need from Fuzz Introspector where we noticed some
discrepancies between the static analysis and the code coverage reports.

Signed-off-by: Arthur Chan <arthur.chan@adalogics.com>

---------

Signed-off-by: Arthur Chan <arthur.chan@adalogics.com>
Signed-off-by: David Korczynski <david@adalogics.com>
Co-authored-by: jonathanmetzman <31354670+jonathanmetzman@users.noreply.github.com>
Co-authored-by: David Korczynski <david@adalogics.com>

Author: 3 people

infra/base-images/base-runner/coverage

@@ -442,6 +442,35 @@ elif [[ $FUZZING_LANGUAGE == "jvm" ]]; then
     cp -r $DUMPS_DIR/${fuzz_target}_classes/* $classes_dir/
   done
 
+  # Dump classes in jar file to dump directory. This action includes all
+  # the classes of the project that are not executed by the fuzzers to
+  # the dump directory. Duplicate classes in the dump directory will be
+  # overwritten. We need to do this to include all possible classes in
+  # the coverage report and avoid duplicate classes from different jar
+  # files which jacoco fails to handle.
+  for jar_file in $(ls $OUT/*.jar)
+  do
+    if [[ $jar_file != $OUT/jazzer* ]]
+    then
+      tempdir=$(mktemp -d)
+      cd $tempdir && jar xvf $jar_file && cd -
+      cp -r $tempdir/* $classes_dir/
+      rm -r $tempdir
+    fi
+  done
+
+  # Clean up files that can create duplicate class names which breaks Jacoco.
+  # Remove META-INF folder because some jar may store duplications of the same
+  # class file in the META-INF for other java versions.
+  find $classes_dir -name "META-INF" | xargs rm -rf
+  # Remove all files that are not a java class because some jar may contain
+  # Kotlin class which has the same name as a java class and Jacoco fail to
+  # distinguish them.
+  find $classes_dir -type f -not -name "*.class" | xargs rm -f
+  # Remove all class files which have a dot in their file name which are normally
+  # used to name a duplication of the legitimate class file.
+  find $classes_dir -type f -name "*.*.class" | xargs rm -f
+
   # Heuristically determine source directories based on Maven structure.
   # Always include the $SRC root as it likely contains the fuzzer sources.
   sourcefiles_args=(--sourcefiles $OUT/$SRC)