fix gradle instrumentation

Author: Rustam Sadykov

utbot-instrumentation/build.gradle

@@ -18,18 +18,17 @@ dependencies {
 jar {
     duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 
-    from sourceSets.main.output
-
     manifest {
         attributes (
                 'Main-Class': 'org.utbot.instrumentation.process.ChildProcessKt',
                 'Premain-Class': 'org.utbot.instrumentation.agent.Agent',
         )
     }
 
-    dependsOn configurations.runtimeClasspath
     from {
-        configurations.runtimeClasspath.findAll { it.name.endsWith('jar') }.collect { zipTree(it) }
+        configurations.compileClasspath.collect {
+            it.isDirectory() ? it : zipTree(it)
+        }
     }
 }
 

utbot-junit-contest/build.gradle

@@ -58,13 +58,14 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-exec', version: '1.2'
     implementation group: 'io.github.microutils', name: 'kotlin-logging', version: kotlin_logging_version
     implementation group: 'org.jsoup', name: 'jsoup', version: '1.6.2'
+    // need for tests
+    implementation group: 'org.mockito', name: 'mockito-core', version: '4.2.0'
+    implementation group: 'org.mockito', name: 'mockito-inline', version: '4.2.0'
+    implementation 'junit:junit:4.13.2'
     testImplementation fileTree(dir: 'src/main/resources/projects/', include: '*/*.jar')
     testImplementation files('src/main/resources/evosuite/evosuite-1.2.0.jar')
     testImplementation files('src/main/resources/evosuite/evosuite-standalone-runtime-1.2.0.jar')
 
-    testImplementation group: 'org.mockito', name: 'mockito-core', version: '4.2.0'
-    testImplementation group: 'org.mockito', name: 'mockito-inline', version: '4.2.0'
-    testImplementation 'junit:junit:4.13.2'
     fetchInstrumentationJar project(path: ':utbot-instrumentation', configuration:'instrumentationArchive')
 }
 
@@ -87,7 +88,7 @@ jar { dependsOn classes
     version '1.0'
 
     from {
-        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
+        sourceSets.main.output + configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
     }
 
     duplicatesStrategy = DuplicatesStrategy.EXCLUDE