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.

stdlib/stdlib.gradle.kts

@@ -10,7 +10,7 @@ plugins {
 // create and publish a self-contained stdlib archive
 // purpose is to provide non-jvm tools/projects with a versioned stdlib
 val stdlibZip by tasks.registering(Zip::class) {
-  destinationDirectory.set(file("$buildDir/libs"))
+  destinationDirectory.set(file("build/libs"))
   archiveBaseName.set("pkl-stdlib")
   archiveVersion.set(project.version as String)
   into("org/pkl/stdlib") {