Update to Gradle 8.6 (#245)

- Fix and clean up the pkl-commons-test build script.
- Change tests to read test packages/certs directly from
  the file system instead of packaging and reading them
  from the class path.
- Update expected checksums of some test packages.
- Fix a conflict between Pkl's and Gradle's
  Kotlin libraries in the pkl-gradle project.
- Fix build deprecation warnings.
- Ensure Gradle distribution integrity with `distributionSha256Sum`.
- Manually verify integrity of Gradle wrapper added by this commit.

buildSrc/src/main/kotlin/pklJavaLibrary.gradle.kts

@@ -55,7 +55,7 @@ val workAroundKotlinGradlePluginBug by tasks.registering {
     // A problem was found with the configuration of task ':pkl-executor:compileJava' (type 'JavaCompile').
     // > Directory '[...]/pkl/pkl-executor/build/classes/kotlin/main'
     // specified for property 'compileKotlinOutputClasses' does not exist.
-    file("$buildDir/classes/kotlin/main").mkdirs()
+    file("build/classes/kotlin/main").mkdirs()
   }
 }