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.

pkl-commons-test/src/main/files/packages/birds@0.5.0/birds@0.5.0.json

@@ -7,7 +7,7 @@
     "fruities": {
       "uri": "package://localhost:12110/fruit@1.0.5",
       "checksums": {
-        "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+        "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
       }
     }
   },

pkl-commons-test/src/main/kotlin/org/pkl/commons/test/PackageServer.kt

@@ -22,6 +22,7 @@ import java.security.KeyStore
 import java.util.concurrent.Executors
 import javax.net.ssl.KeyManagerFactory
 import javax.net.ssl.SSLContext
+import kotlin.io.path.inputStream
 import kotlin.io.path.isRegularFile
 import org.pkl.commons.createParentDirectories
 import org.pkl.commons.deleteRecursively
@@ -66,26 +67,20 @@ class PackageServer : AutoCloseable {
     // Modified by RequestRewritingClient if testPort is set.
     private const val PORT = 12110
 
-    // When tests are run via Gradle (i.e. from ./gradlew check), resources are packaged into a jar.
-    // When run directly in IntelliJ, resources are just directories.
-    private val packagesDir: Path by lazy {
-      val uri = PackageServer::class.java.getResource("packages")!!.toURI()
-      try {
-        Path.of(uri)
-      } catch (e: FileSystemNotFoundException) {
-        FileSystems.newFileSystem(uri, mapOf<String, String>())
-        Path.of(uri)
-      }
-    }
+    private val packagesDir: Path =
+      FileTestUtils.rootProjectDir.resolve("pkl-commons-test/build/test-packages")
 
     private val simpleHttpsConfigurator by lazy {
       val sslContext =
         SSLContext.getInstance("SSL").apply {
           val pass = "password".toCharArray()
-          val keystore = PackageServer::class.java.getResource("/localhost.p12")!!
-          val ks = KeyStore.getInstance("PKCS12").apply { load(keystore.openStream(), pass) }
-          val kmf = KeyManagerFactory.getInstance("SunX509").apply { init(ks, pass) }
-          init(kmf.keyManagers, null, null)
+          val keystore =
+            FileTestUtils.rootProjectDir.resolve("pkl-commons-test/build/keystore/localhost.p12")
+          keystore.inputStream().use { stream ->
+            val ks = KeyStore.getInstance("PKCS12").apply { load(stream, pass) }
+            val kmf = KeyManagerFactory.getInstance("SunX509").apply { init(ks, pass) }
+            init(kmf.keyManagers, null, null)
+          }
         }
       val engine = sslContext.createSSLEngine()
       object : HttpsConfigurator(sslContext) {