diff --git a/.github/workflows/gradle.yml b/.github/workflows/gradle.yml
index 37bbdbf..a8189eb 100644
--- a/.github/workflows/gradle.yml
+++ b/.github/workflows/gradle.yml
@@ -11,8 +11,19 @@ on:
 
 jobs:
   build:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: 'ignore warnings'
+            additional-check-args: ''
+            continue-on-error: false
+          - name: 'fail on warning'
+            additional-check-args: '--warning-mode=fail -PfailOnWarning'
+            continue-on-error: true
 
     runs-on: ubuntu-latest
+    continue-on-error: ${{ matrix.continue-on-error }}
 
     steps:
     - uses: actions/checkout@v2
@@ -24,4 +35,4 @@ jobs:
     - name: Grant execute permission for gradlew
       run: chmod +x gradlew
     - name: Build with Gradle
-      run: ./gradlew --info --stacktrace check
+      run: ./gradlew --info --stacktrace check ${{ matrix.additional-check-args }}
diff --git a/build.gradle b/build.gradle
index abbc5eb..8e122bd 100644
--- a/build.gradle
+++ b/build.gradle
@@ -104,6 +104,8 @@ task functionalTest(type: Test) {
         showStandardStreams = System.env.CI == 'true'
     }
 
+    systemProperty 'failOnWarning', project.hasProperty('failOnWarning')
+
     mustRunAfter crossScalaVersionTest
 }
 check.dependsOn functionalTest
@@ -206,4 +208,4 @@ idea.project.settings {
     taskTriggers {
         beforeBuild fixIdeaPluginClasspath, pluginUnderTestMetadata
     }
-}
\ No newline at end of file
+}
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index 5c2d1cf..7454180 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 69a9715..ffed3a2 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
index b0d6d0a..1b6c787 100755
--- a/gradlew
+++ b/gradlew
@@ -1,13 +1,13 @@
-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+#      https://www.apache.org/licenses/LICENSE-2.0
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
@@ -17,78 +17,113 @@
 #
 
 ##############################################################################
-##
-##  Gradle start up script for UN*X
-##
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
+
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
+APP_BASE_NAME=${0##*/}
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
+
 # Determine the Java command to use to start the JVM.
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -97,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
+    JAVACMD=java
     which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
@@ -105,84 +140,95 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
 fi
 
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
     # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
         fi
-        i=$((i+1))
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
     done
-    case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
-    esac
 fi
 
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=$(save "$@")
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
index 15e1ee3..ac1b06f 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -5,7 +5,7 @@
 @rem you may not use this file except in compliance with the License.
 @rem You may obtain a copy of the License at
 @rem
-@rem      http://www.apache.org/licenses/LICENSE-2.0
+@rem      https://www.apache.org/licenses/LICENSE-2.0
 @rem
 @rem Unless required by applicable law or agreed to in writing, software
 @rem distributed under the License is distributed on an "AS IS" BASIS,
@@ -29,6 +29,9 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
@@ -37,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if "%ERRORLEVEL%" == "0" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -51,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -61,28 +64,14 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
 set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
+
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell
diff --git a/src/crossScalaVersionTest/java/org/scoverage/ScalaCrossVersionAggregationTest.java b/src/crossScalaVersionTest/java/org/scoverage/ScalaCrossVersionAggregationTest.java
index e6c3bf3..a7b7e5b 100644
--- a/src/crossScalaVersionTest/java/org/scoverage/ScalaCrossVersionAggregationTest.java
+++ b/src/crossScalaVersionTest/java/org/scoverage/ScalaCrossVersionAggregationTest.java
@@ -30,7 +30,7 @@ public void checkAndAggregateAll() throws Exception {
     private void assertAggregationFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "2_12/src/main/scala/org/hello/World2_12.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "2_13/src/main/scala/org/hello/World2_13.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World2_12.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World2_13.scala.html").exists());
     }
 }
diff --git a/src/crossScalaVersionTest/java/org/scoverage/ScalaVersionTest.java b/src/crossScalaVersionTest/java/org/scoverage/ScalaVersionTest.java
index 55a15c8..657ca8e 100644
--- a/src/crossScalaVersionTest/java/org/scoverage/ScalaVersionTest.java
+++ b/src/crossScalaVersionTest/java/org/scoverage/ScalaVersionTest.java
@@ -27,6 +27,6 @@ public void report() throws Exception {
 
         File reportDir = reportDir(projectDir().toPath().resolve(scalaVersion).toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/World" + scalaVersion + ".scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/World" + scalaVersion + ".scala.html").exists());
     }
-}
\ No newline at end of file
+}
diff --git a/src/functionalTest/java/org/scoverage/ScalaJavaAnnotationProcessorTest.java b/src/functionalTest/java/org/scoverage/ScalaJavaAnnotationProcessorTest.java
index ba82eae..c4c2e38 100644
--- a/src/functionalTest/java/org/scoverage/ScalaJavaAnnotationProcessorTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaJavaAnnotationProcessorTest.java
@@ -44,13 +44,13 @@ private void assertAllReportFilesExist() {
 
     private void assertAggregationFilesExist() {
 
-        Assert.assertTrue(resolve(reportDir(), "mixed_scala_java/src/main/scala/org/hello/WorldScala.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/WorldScala.scala.html").exists());
     }
 
     private void assertMixedScalaJavaReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("mixed_scala_java").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/WorldScala.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/WorldScala.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScalaJavaMultiModuleTest.java b/src/functionalTest/java/org/scoverage/ScalaJavaMultiModuleTest.java
index 8a35add..2b09933 100644
--- a/src/functionalTest/java/org/scoverage/ScalaJavaMultiModuleTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaJavaMultiModuleTest.java
@@ -46,21 +46,21 @@ private void assertAllReportFilesExist() {
 
     private void assertAggregationFilesExist() {
 
-        Assert.assertTrue(resolve(reportDir(), "scala_only/src/main/scala/org/hello/WorldScalaOnly.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "mixed_scala_java/src/main/scala/org/hello/WorldScala.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/WorldScalaOnly.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/WorldScala.scala.html").exists());
     }
 
     private void assertScalaOnlyReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("scala_only").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/WorldScalaOnly.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/WorldScalaOnly.scala.html").exists());
     }
 
     private void assertMixedScalaJavaReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("mixed_scala_java").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/WorldScala.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/WorldScala.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScalaMultiModuleTest.java b/src/functionalTest/java/org/scoverage/ScalaMultiModuleTest.java
index 87f5c02..5da6f60 100644
--- a/src/functionalTest/java/org/scoverage/ScalaMultiModuleTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaMultiModuleTest.java
@@ -297,35 +297,35 @@ private void assertAllReportFilesExist() {
 
     private void assertAggregationFilesExist() {
 
-        Assert.assertTrue(resolve(reportDir(), "a/src/main/scala/org/hello/a/WorldA.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "b/src/main/scala/org/hello/b/WorldB.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "common/src/main/scala/org/hello/common/WorldCommon.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/a/WorldA.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/b/WorldB.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/common/WorldCommon.scala.html").exists());
     }
 
     private void assertRootReportFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World.scala.html").exists());
     }
 
     private void assertAReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("a").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/a/WorldA.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/a/WorldA.scala.html").exists());
     }
 
     private void assertBReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("b").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/b/WorldB.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/b/WorldB.scala.html").exists());
     }
 
     private void assertCommonReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("common").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/common/WorldCommon.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/common/WorldCommon.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScalaMultiModuleWithMultipleTestTasksTest.java b/src/functionalTest/java/org/scoverage/ScalaMultiModuleWithMultipleTestTasksTest.java
index 49d0bc1..dc84e1f 100644
--- a/src/functionalTest/java/org/scoverage/ScalaMultiModuleWithMultipleTestTasksTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaMultiModuleWithMultipleTestTasksTest.java
@@ -294,35 +294,35 @@ private void assertAllReportFilesExist() {
 
     private void assertAggregationFilesExist() {
 
-        Assert.assertTrue(resolve(reportDir(), "a/src/main/scala/org/hello/a/WorldA.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "b/src/main/scala/org/hello/b/WorldB.scala.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "common/src/main/scala/org/hello/common/WorldCommon.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/a/WorldA.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/b/WorldB.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/common/WorldCommon.scala.html").exists());
     }
 
     private void assertRootReportFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World.scala.html").exists());
     }
 
     private void assertAReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("a").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/a/WorldA.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/a/WorldA.scala.html").exists());
     }
 
     private void assertBReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("b").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/b/WorldB.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/b/WorldB.scala.html").exists());
     }
 
     private void assertCommonReportFilesExist() {
 
         File reportDir = reportDir(projectDir().toPath().resolve("common").toFile());
         Assert.assertTrue(resolve(reportDir, "index.html").exists());
-        Assert.assertTrue(resolve(reportDir, "src/main/scala/org/hello/common/WorldCommon.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir, "org/hello/common/WorldCommon.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScalaSingleModuleTest.java b/src/functionalTest/java/org/scoverage/ScalaSingleModuleTest.java
index de9da68..19e0e82 100644
--- a/src/functionalTest/java/org/scoverage/ScalaSingleModuleTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaSingleModuleTest.java
@@ -91,7 +91,7 @@ public void reportScoverageWithExcludedClasses() throws Exception {
         result.assertTaskDoesntExist(ScoveragePlugin.getAGGREGATE_NAME());
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertFalse(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertFalse(resolve(reportDir(), "org/hello/World.scala.html").exists());
         assertCoverage(100.0); // coverage is 100 since no classes are covered
 
         // compiled class should exist in the default classes directory, but not in scoverage
@@ -125,7 +125,7 @@ public void reportScoverageWithoutNormalCompilationAndWithExcludedClasses() thro
                 "-PexcludedFile=.*", "-P" + ScoveragePlugin.getSCOVERAGE_COMPILE_ONLY_PROPERTY());
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertFalse(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertFalse(resolve(reportDir(), "org/hello/World.scala.html").exists());
         assertCoverage(100.0); // coverage is 100 since no classes are covered
 
         // compiled class should exist in the default classes directory, but not in scoverage
@@ -136,6 +136,6 @@ public void reportScoverageWithoutNormalCompilationAndWithExcludedClasses() thro
     private void assertReportFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithDependencyManagerTest.java b/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithDependencyManagerTest.java
index e7f701a..3ce3b63 100644
--- a/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithDependencyManagerTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithDependencyManagerTest.java
@@ -26,6 +26,6 @@ public void checkScoverage() throws Exception {
     private void assertReportFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World.scala.html").exists());
     }
-}
\ No newline at end of file
+}
diff --git a/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithMultipleTestTasksTest.java b/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithMultipleTestTasksTest.java
index 0511eb5..cba1c6a 100644
--- a/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithMultipleTestTasksTest.java
+++ b/src/functionalTest/java/org/scoverage/ScalaSingleModuleWithMultipleTestTasksTest.java
@@ -109,7 +109,7 @@ public void reportScoverageWithExcludedClasses() throws Exception {
         result.assertTaskDoesntExist(ScoveragePlugin.getAGGREGATE_NAME());
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertFalse(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertFalse(resolve(reportDir(), "org/hello/World.scala.html").exists());
         assertCoverage(100.0); // coverage is 100 since no classes are covered
 
         // compiled class should exist in the default classes directory, but not in scoverage
@@ -143,7 +143,7 @@ public void reportScoverageWithoutNormalCompilationAndWithExcludedClasses() thro
                 "-PexcludedFile=.*", "-P" + ScoveragePlugin.getSCOVERAGE_COMPILE_ONLY_PROPERTY());
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertFalse(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertFalse(resolve(reportDir(), "org/hello/World.scala.html").exists());
         assertCoverage(100.0); // coverage is 100 since no classes are covered
 
         // compiled class should exist in the default classes directory, but not in scoverage
@@ -155,6 +155,6 @@ public void reportScoverageWithoutNormalCompilationAndWithExcludedClasses() thro
     private void assertReportFilesExist() {
 
         Assert.assertTrue(resolve(reportDir(), "index.html").exists());
-        Assert.assertTrue(resolve(reportDir(), "src/main/scala/org/hello/World.scala.html").exists());
+        Assert.assertTrue(resolve(reportDir(), "org/hello/World.scala.html").exists());
     }
 }
diff --git a/src/functionalTest/java/org/scoverage/ScoverageFunctionalTest.java b/src/functionalTest/java/org/scoverage/ScoverageFunctionalTest.java
index e08d1e5..051b6bb 100644
--- a/src/functionalTest/java/org/scoverage/ScoverageFunctionalTest.java
+++ b/src/functionalTest/java/org/scoverage/ScoverageFunctionalTest.java
@@ -127,7 +127,11 @@ private void configureArguments(String... arguments) {
         fullArguments.add("-PjunitVersion=5.3.2");
         fullArguments.add("-PjunitPlatformVersion=1.3.2");
         fullArguments.add("-PscalatestVersion=3.0.8");
-        fullArguments.add("--warning-mode=all");
+        if (Boolean.parseBoolean(System.getProperty("failOnWarning"))) {
+            fullArguments.add("--warning-mode=fail");
+        } else {
+            fullArguments.add("--warning-mode=all");
+        }
         fullArguments.addAll(Arrays.asList(arguments));
 
         runner.withArguments(fullArguments);
diff --git a/src/functionalTest/resources/projects/scala-java-annotation-processor/build.gradle b/src/functionalTest/resources/projects/scala-java-annotation-processor/build.gradle
index 9e5797f..c67b12d 100644
--- a/src/functionalTest/resources/projects/scala-java-annotation-processor/build.gradle
+++ b/src/functionalTest/resources/projects/scala-java-annotation-processor/build.gradle
@@ -6,7 +6,7 @@ description = 'a multi-module Scala and Java project using a Java annotation pro
 
 allprojects {
     repositories {
-        jcenter()
+        mavenCentral()
     }
 }
 
diff --git a/src/main/groovy/org/scoverage/ScoverageAggregate.groovy b/src/main/groovy/org/scoverage/ScoverageAggregate.groovy
index b445e29..9815dd1 100644
--- a/src/main/groovy/org/scoverage/ScoverageAggregate.groovy
+++ b/src/main/groovy/org/scoverage/ScoverageAggregate.groovy
@@ -1,19 +1,28 @@
 package org.scoverage
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.FileCollection
 import org.gradle.api.provider.ListProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Nested
 import org.gradle.api.tasks.OutputDirectory
+import org.gradle.api.tasks.PathSensitive
 import org.gradle.api.tasks.TaskAction
 import scoverage.report.CoverageAggregator
 
+import static org.gradle.api.tasks.PathSensitivity.RELATIVE
+
 class ScoverageAggregate extends DefaultTask {
 
     @Nested
     ScoverageRunner runner
 
+    @InputFiles
+    @PathSensitive(RELATIVE)
+    final Property<FileCollection> sources = project.objects.property(FileCollection)
+
     @OutputDirectory
     final Property<File> reportDir = project.objects.property(File)
 
@@ -52,7 +61,7 @@ class ScoverageAggregate extends DefaultTask {
 
             if (coverage.nonEmpty()) {
                 new ScoverageWriter(project.logger).write(
-                        project.projectDir,
+                        sources.get().getFiles(),
                         reportDir.get(),
                         coverage.get(),
                         sourceEncoding.get(),
diff --git a/src/main/groovy/org/scoverage/ScoverageExtension.groovy b/src/main/groovy/org/scoverage/ScoverageExtension.groovy
index e106306..210a825 100644
--- a/src/main/groovy/org/scoverage/ScoverageExtension.groovy
+++ b/src/main/groovy/org/scoverage/ScoverageExtension.groovy
@@ -28,8 +28,6 @@ class ScoverageExtension {
     final Property<File> dataDir
     /** a directory to write final output to */
     final Property<File> reportDir
-    /** sources to highlight */
-    final Property<File> sources
     /** range positioning for highlighting */
     final Property<Boolean> highlighting
     /** regex for each excluded package */
@@ -61,9 +59,6 @@ class ScoverageExtension {
 
         scoverageScalaVersion = project.objects.property(String)
 
-        sources = project.objects.property(File)
-        sources.set(project.projectDir)
-
         dataDir = project.objects.property(File)
         dataDir.set(new File(project.buildDir, 'scoverage'))
 
diff --git a/src/main/groovy/org/scoverage/ScoveragePlugin.groovy b/src/main/groovy/org/scoverage/ScoveragePlugin.groovy
index ae5d68e..4f1ba18 100644
--- a/src/main/groovy/org/scoverage/ScoveragePlugin.groovy
+++ b/src/main/groovy/org/scoverage/ScoveragePlugin.groovy
@@ -29,7 +29,8 @@ class ScoveragePlugin implements Plugin<PluginAware> {
 
     static final String DEFAULT_REPORT_DIR = 'reports' + File.separatorChar + 'scoverage'
 
-    private final ConcurrentHashMap<Task, Set<? extends Task>> taskDependencies = new ConcurrentHashMap<>()
+    private final ConcurrentHashMap<Task, Set<? extends Task>> crossProjectTaskDependencies = new ConcurrentHashMap<>()
+    private final ConcurrentHashMap<Task, Set<? extends Task>> sameProjectTaskDependencies = new ConcurrentHashMap<>()
 
     @Override
     void apply(PluginAware pluginAware) {
@@ -124,7 +125,7 @@ class ScoveragePlugin implements Plugin<PluginAware> {
                     group = 'verification'
                     runner = scoverageRunner
                     reportDir = taskReportDir
-                    sources = extension.sources
+                    sources = originalSourceSet.scala.getSourceDirectories()
                     dataDir = extension.dataDir
                     sourceEncoding.set(detectedSourceEncoding)
                     coverageOutputCobertura = extension.coverageOutputCobertura
@@ -143,6 +144,7 @@ class ScoveragePlugin implements Plugin<PluginAware> {
                 group = 'verification'
                 runner = scoverageRunner
                 reportDir = extension.reportDir
+                sources = originalSourceSet.scala.getSourceDirectories()
                 dirsToAggregateFrom = dataDirs
                 sourceEncoding.set(detectedSourceEncoding)
                 deleteReportsOnAggregation = false
@@ -194,11 +196,16 @@ class ScoveragePlugin implements Plugin<PluginAware> {
 
                 originalCompileTask.enabled = false;
                 compileTask.destinationDirectory = originalCompileTask.destinationDirectory
-                originalJarTask.mustRunAfter(compileTask)
+
+                project.getTasks().each {
+                    if (recursiveDependenciesOf(it, true).contains(originalCompileTask)) {
+                        it.dependsOn(compileTask)
+                    }
+                }
 
                 // make this project's scoverage compilation depend on scoverage compilation of any other project
                 // which this project depends on its normal compilation
-                def originalCompilationDependencies = recursiveDependenciesOf(compileTask).findAll {
+                def originalCompilationDependencies = recursiveDependenciesOf(compileTask, false).findAll {
                     it instanceof ScalaCompile
                 }
                 originalCompilationDependencies.each {
@@ -299,6 +306,10 @@ class ScoveragePlugin implements Plugin<PluginAware> {
                         }
                     }
                     def allReportTasks = childReportTasks + globalReportTask.get()
+                    def allSources = project.objects.fileCollection()
+                    allReportTasks.each {
+                        allSources = allSources.plus(it.sources.get())
+                    }
                     def aggregationTask = project.tasks.create(AGGREGATE_NAME, ScoverageAggregate) {
                         def dataDirs = allReportTasks.findResults { it.dirsToAggregateFrom.get() }.flatten()
                         onlyIf {
@@ -308,6 +319,7 @@ class ScoveragePlugin implements Plugin<PluginAware> {
                         group = 'verification'
                         runner = scoverageRunner
                         reportDir = extension.reportDir
+                        sources = allSources
                         sourceEncoding.set(detectedSourceEncoding)
                         dirsToAggregateFrom = dataDirs
                         deleteReportsOnAggregation = extension.deleteReportsOnAggregation
@@ -376,16 +388,22 @@ class ScoveragePlugin implements Plugin<PluginAware> {
         }
     }
 
-    private Set<? extends Task> recursiveDependenciesOf(Task task) {
-        if (!taskDependencies.containsKey(task)) {
+    private Set<? extends Task> recursiveDependenciesOf(Task task, boolean sameProjectOnly) {
+        def cache = sameProjectOnly ? sameProjectTaskDependencies : crossProjectTaskDependencies
+        if (!cache.containsKey(task)) {
             def directDependencies = task.getTaskDependencies().getDependencies(task)
-            def nestedDependencies = directDependencies.collect { recursiveDependenciesOf(it) }.flatten()
+            if (sameProjectOnly) {
+                directDependencies = directDependencies.findAll {
+                    it.project == task.project
+                }
+            }
+            def nestedDependencies = directDependencies.collect { recursiveDependenciesOf(it, sameProjectOnly) }.flatten()
             def dependencies = directDependencies + nestedDependencies
 
-            taskDependencies.put(task, dependencies)
+            cache.put(task, dependencies)
             return dependencies
         } else {
-            return taskDependencies.get(task)
+            return cache.get(task)
         }
     }
 }
diff --git a/src/main/groovy/org/scoverage/ScoverageReport.groovy b/src/main/groovy/org/scoverage/ScoverageReport.groovy
index e95f547..8a15aab 100644
--- a/src/main/groovy/org/scoverage/ScoverageReport.groovy
+++ b/src/main/groovy/org/scoverage/ScoverageReport.groovy
@@ -1,10 +1,12 @@
 package org.scoverage
 
 import org.gradle.api.DefaultTask
+import org.gradle.api.file.FileCollection
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.CacheableTask
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.InputFiles
 import org.gradle.api.tasks.Nested
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.PathSensitive
@@ -23,9 +25,9 @@ class ScoverageReport extends DefaultTask {
     @PathSensitive(RELATIVE)
     final Property<File> dataDir = project.objects.property(File)
 
-    @InputDirectory
+    @InputFiles
     @PathSensitive(RELATIVE)
-    final Property<File> sources = project.objects.property(File)
+    final Property<FileCollection> sources = project.objects.property(FileCollection)
 
     @OutputDirectory
     final Property<File> reportDir = project.objects.property(File)
@@ -54,7 +56,7 @@ class ScoverageReport extends DefaultTask {
                 project.logger.info("[scoverage] Could not find coverage file, skipping...")
             } else {
                 new ScoverageWriter(project.logger).write(
-                        sources.get(),
+                        sources.get().getFiles(),
                         reportDir.get(),
                         coverage.get(),
                         sourceEncoding.get(),
diff --git a/src/main/groovy/org/scoverage/ScoverageWriter.java b/src/main/groovy/org/scoverage/ScoverageWriter.java
index 2f95a51..1e09105 100644
--- a/src/main/groovy/org/scoverage/ScoverageWriter.java
+++ b/src/main/groovy/org/scoverage/ScoverageWriter.java
@@ -1,14 +1,23 @@
 package org.scoverage;
 
 import org.gradle.api.logging.Logger;
+import scala.Option;
 import scala.Some;
+import scala.collection.immutable.Seq;
+import scala.collection.mutable.Buffer;
 import scoverage.Constants;
 import scoverage.Coverage;
 import scoverage.report.CoberturaXmlWriter;
 import scoverage.report.ScoverageHtmlWriter;
 import scoverage.report.ScoverageXmlWriter;
+import scala.collection.JavaConverters;
 
 import java.io.File;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Set;
 
 /**
  * Util for generating and saving coverage files.
@@ -26,7 +35,7 @@ public ScoverageWriter(Logger logger) {
     /**
      * Generates all reports from given data.
      *
-     * @param sourceDir               directory with project sources
+     * @param sourceDirs               directories with project sources
      * @param reportDir               directory for generate reports
      * @param coverage                coverage data
      * @param sourceEncoding          the encoding of the source files
@@ -35,21 +44,33 @@ public ScoverageWriter(Logger logger) {
      * @param coverageOutputHTML      switch for Scoverage HTML output
      * @param coverageDebug           switch for Scoverage Debug output
      */
-    public void write(File sourceDir,
+    public void write(Set<File> sourceDirs,
                              File reportDir,
                              Coverage coverage,
                              String sourceEncoding,
                              Boolean coverageOutputCobertura,
                              Boolean coverageOutputXML,
                              Boolean coverageOutputHTML,
-                             Boolean coverageDebug) {
+                             Boolean coverageDebug) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, InstantiationException {
 
         logger.info("[scoverage] Generating scoverage reports...");
 
         reportDir.mkdirs();
 
+        Object scalaBuffer = Class.forName("scala.collection.JavaConverters")
+                .getMethod("asScalaBuffer", java.util.List.class)
+                .invoke(null, new ArrayList<>(sourceDirs));
+        Object sourceDirsSeq = scalaBuffer.getClass().getMethod("toIndexedSeq").invoke(scalaBuffer);
+
         if (coverageOutputCobertura) {
-            new CoberturaXmlWriter(sourceDir, reportDir).write(coverage);
+            Constructor<CoberturaXmlWriter> cst;
+            try {
+                cst = CoberturaXmlWriter.class.getConstructor(Class.forName("scala.collection.immutable.Seq"), File.class);
+            } catch (NoSuchMethodException | ClassNotFoundException e) {
+                cst = CoberturaXmlWriter.class.getConstructor(Class.forName("scala.collection.Seq"), File.class);
+            }
+            CoberturaXmlWriter writer = cst.newInstance(sourceDirsSeq, reportDir);
+            writer.write(coverage);
             logger.info("[scoverage] Written Cobertura XML report to " +
                 reportDir.getAbsolutePath() +
                 File.separator +
@@ -57,13 +78,21 @@ public void write(File sourceDir,
         }
 
         if (coverageOutputXML) {
-            new ScoverageXmlWriter(sourceDir, reportDir, /* debug = */ false).write(coverage);
+            Constructor<ScoverageXmlWriter> cst;
+            try {
+                cst = ScoverageXmlWriter.class.getConstructor(Class.forName("scala.collection.immutable.Seq"), File.class, boolean.class);
+            } catch (NoSuchMethodException | ClassNotFoundException e) {
+                cst = ScoverageXmlWriter.class.getConstructor(Class.forName("scala.collection.Seq"), File.class, boolean.class);
+            }
+            ScoverageXmlWriter writer = cst.newInstance(sourceDirsSeq, reportDir, false);
+            writer.write(coverage);
             logger.info("[scoverage] Written XML report to " +
                 reportDir.getAbsolutePath() +
                 File.separator +
                 Constants.XMLReportFilename());
             if (coverageDebug) {
-                new ScoverageXmlWriter(sourceDir, reportDir, /* debug = */ true).write(coverage);
+                ScoverageXmlWriter writerDebug = cst.newInstance(sourceDirsSeq, reportDir, true);
+                writerDebug.write(coverage);
                 logger.info("[scoverage] Written XML report with debug information to " +
                     reportDir.getAbsolutePath() +
                     File.separator +
@@ -72,7 +101,14 @@ public void write(File sourceDir,
         }
 
         if (coverageOutputHTML) {
-            new ScoverageHtmlWriter(new File[]{sourceDir}, reportDir, new Some<>(sourceEncoding)).write(coverage);
+            Constructor<ScoverageHtmlWriter> cst;
+            try {
+                cst = ScoverageHtmlWriter.class.getConstructor(Class.forName("scala.collection.immutable.Seq"), File.class, Option.class);
+            } catch (NoSuchMethodException | ClassNotFoundException e) {
+                cst = ScoverageHtmlWriter.class.getConstructor(Class.forName("scala.collection.Seq"), File.class, Option.class);
+            }
+            ScoverageHtmlWriter writer = cst.newInstance(sourceDirsSeq, reportDir, new Some<>(sourceEncoding));
+            writer.write(coverage);
             logger.info("[scoverage] Written HTML report to " +
                 reportDir.getAbsolutePath() +
                 File.separator +