Also clean newly added files.

Some patches could add new file and after hard reset they are not
deleted. This leads to patch apply failure.

Updated JGit otherwise clean command was not working properly.

gradle/verification-metadata.xml

@@ -2171,6 +2171,12 @@
             <sha256 value="b19204331ac6e204befaf508a68f52ec6b4638d9d9bacddbebd435f9c4d500f2" origin="Generated by Gradle"/>
          </artifact>
       </component>
+      <component group="com.googlecode.javaewah" name="JavaEWAH" version="1.1.13">
+         <artifact name="JavaEWAH-1.1.13.jar">
+            <md5 value="a1eb305e5cc5bba238d4360e3139abb4" origin="Generated by Gradle"/>
+            <sha256 value="4c0fda2b1d317750d7ea324e36c70b2bc48310c0aaae67b98df0915d696d7111" origin="Generated by Gradle"/>
+         </artifact>
+      </component>
       <component group="com.googlecode.json-simple" name="json-simple" version="1.1">
          <artifact name="json-simple-1.1.jar">
             <md5 value="eb342044fc56be9ba49fbfc9789f1bb5" origin="Generated by Gradle"/>
@@ -6416,6 +6422,12 @@
             <sha256 value="dabf8369f0cdf8cf17b7f7da4bda9320c570bb754c88e0beb7b852812cf5cd25" origin="Generated by Gradle"/>
          </artifact>
       </component>
+      <component group="org.eclipse.jgit" name="org.eclipse.jgit" version="6.4.0.202211300538-r">
+         <artifact name="org.eclipse.jgit-6.4.0.202211300538-r.jar">
+            <md5 value="2750720ae43f9cb254e6349080bf9d70" origin="Generated by Gradle"/>
+            <sha256 value="c1487989eadb53bd58a47b72fb069636397bb8dfedf21387a40a86c3e7b2faac" origin="Generated by Gradle"/>
+         </artifact>
+      </component>
       <component group="org.eclipse.sisu" name="org.eclipse.sisu.inject" version="0.3.5">
          <artifact name="org.eclipse.sisu.inject-0.3.5.jar">
             <md5 value="1b296b0ddd911ed3750b3df93b395cd5" origin="Generated by Gradle"/>

libraries/tools/gradle/regression-benchmark-templates/build.gradle.kts

@@ -5,7 +5,7 @@ plugins {
 dependencies {
     implementation("org.jetbrains.kotlin:kotlin-scripting-common")
     implementation("com.squareup.okhttp3:okhttp:4.9.0")
-    implementation("org.eclipse.jgit:org.eclipse.jgit:5.13.0.202109080827-r")
+    implementation("org.eclipse.jgit:org.eclipse.jgit:6.4.0.202211300538-r")
     implementation("org.slf4j:slf4j-nop:1.7.32")
     implementation("org.jetbrains.kotlinx:dataframe:0.8.1")
 }

libraries/tools/gradle/regression-benchmark-templates/src/main/kotlin/org/jetbrains/kotlin/gradle/benchmark/BenchmarkTemplate.kt

@@ -123,19 +123,25 @@ abstract class BenchmarkTemplate(
         patch: InputStream
     ) {
         println("Applying patch $patchName to repository")
-        Git.open(projectRepoDir)
+        val git = Git.open(projectRepoDir)
-            .apply()
+        git.apply()
             .setPatch(patch)
             .call()
+        git.close()
     }
 
     fun repoReset() {
         println("Hard resetting project repo")
-        Git.open(projectRepoDir)
+        val git = Git.open(projectRepoDir)
-            .reset()
+        git.reset()
             .setMode(ResetCommand.ResetType.HARD)
             .setProgressMonitor(gitOperationsPrinter)
             .call()
+        git.clean()
+            .setCleanDirectories(true)
+            .setForce(true)
+            .call()
+        git.close()
     }
 
     private fun runBenchmark(