[Maven] Filter duplicated source roots to avoid multiple module declarations exception

After fixing of KT-13995 (99de93bb) there is a case when several maven plugins register the same source roots twice, which leads to the Kotlin compiler exception "Too many source module declarations found". kotlin-maven-plugin should take care of what it passes to the Kotlin compiler to avoid it

#KT-58048 Fixed

Merge-request: KT-MR-9716
Merged-by: Aleksei Cherepanov <aleksei.cherepanov@jetbrains.com>

libraries/tools/kotlin-maven-plugin-test/src/it/java9/test-sourceRootsRegisteredSeveralTimes/pom.xml

@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.jetbrains.kotlin</groupId>
+    <artifactId>test-sourceRootsRegisteredSeveralTimes</artifactId>
+    <version>1.0-SNAPSHOT</version>
+
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.1</version>
+        </dependency>
+        <dependency>
+            <groupId>org.jetbrains.kotlin</groupId>
+            <artifactId>kotlin-stdlib</artifactId>
+            <version>${kotlin.version}</version>
+        </dependency>
+    </dependencies>
+
+    <properties>
+        <kotlin.compiler.incremental>true</kotlin.compiler.incremental>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
+        <maven.compiler.parameters>true</maven.compiler.parameters>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>kotlin-maven-plugin</artifactId>
+                <groupId>org.jetbrains.kotlin</groupId>
+                <version>${kotlin.version}</version>
+                <executions>
+                    <execution>
+                        <id>compile</id>
+                        <goals>
+                            <goal>compile</goal>
+                        </goals>
+                        <configuration>
+                            <sourceDirs>
+                                <sourceDir>${project.basedir}/src/main/kotlin</sourceDir>
+                                <sourceDir>${project.basedir}/src/main/java</sourceDir>
+                            </sourceDirs>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>test-compile</id>
+                        <goals>
+                            <goal>test-compile</goal>
+                        </goals>
+                        <configuration>
+                            <sourceDirs>
+                                <sourceDir>${project.basedir}/src/test/kotlin</sourceDir>
+                                <sourceDir>${project.basedir}/src/test/java</sourceDir>
+                            </sourceDirs>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.10.1</version>
+                <configuration>
+                    <source>1.9</source>
+                    <target>1.9</target>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>default-compile</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <id>default-testCompile</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <id>java-compile</id>
+                        <phase>compile</phase>
+                        <goals>
+                            <goal>compile</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>java-test-compile</id>
+                        <phase>test-compile</phase>
+                        <goals>
+                            <goal>testCompile</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>

libraries/tools/kotlin-maven-plugin-test/src/it/java9/test-sourceRootsRegisteredSeveralTimes/src/main/java/foo/bar/Foo.java

@@ -0,0 +1,4 @@
+package foo.bar;
+
+public class Foo {
+}

libraries/tools/kotlin-maven-plugin-test/src/it/java9/test-sourceRootsRegisteredSeveralTimes/src/main/java/module-info.java

@@ -0,0 +1,6 @@
+module foo.bar {
+  exports foo.bar;
+
+
+  requires kotlin.stdlib;
+}

libraries/tools/kotlin-maven-plugin-test/src/it/java9/test-sourceRootsRegisteredSeveralTimes/src/main/kotlin/koo/bar/Koo.kt

@@ -0,0 +1,4 @@
+package koo.bar
+
+class Koo {
+}

libraries/tools/kotlin-maven-plugin-test/src/it/java9/test-sourceRootsRegisteredSeveralTimes/verify.bsh

@@ -0,0 +1,6 @@
+import java.io.*;
+
+File file = new File(basedir, "target/test-sourceRootsRegisteredSeveralTimes-1.0-SNAPSHOT.jar");
+if (!file.exists() || !file.isFile()) {
+    throw new FileNotFoundException("Could not find generated JAR: " + file);
+}

libraries/tools/kotlin-maven-plugin/src/main/java/org/jetbrains/kotlin/maven/KotlinCompileMojoBase.java

@@ -37,10 +37,12 @@ import org.jetbrains.kotlin.config.KotlinCompilerVersion;
 import org.jetbrains.kotlin.config.Services;
 
 import java.io.File;
+import java.io.IOException;
 import java.lang.reflect.Field;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.util.stream.Collectors;
 
 import static org.jetbrains.kotlin.maven.Util.joinArrays;
 
@@ -79,10 +81,12 @@ public abstract class KotlinCompileMojoBase<A extends CommonCompilerArguments> e
     private boolean multiPlatform = false;
 
     protected List<String> getSourceFilePaths() {
-        List<String> list = new ArrayList<>();
-        if (sourceDirs != null && !sourceDirs.isEmpty()) list.addAll(sourceDirs);
-        list.addAll(project.getCompileSourceRoots());
-        return list;
+        List<String> sourceFilePaths = new ArrayList<>();
+        if (sourceDirs != null && !sourceDirs.isEmpty()) sourceFilePaths.addAll(sourceDirs);
+        sourceFilePaths.addAll(project.getCompileSourceRoots());
+
+        return sourceFilePaths.stream().map(path -> new File(path).toPath().normalize().toString())
+                .distinct().collect(Collectors.toList());
     }
 
     @NotNull