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-cli/pkl-cli.gradle.kts

@@ -56,11 +56,11 @@ dependencies {
 
   testImplementation(projects.pklCommonsTest)
 
-  stagedMacAmd64Executable(files("$buildDir/executable/pkl-macos-amd64"))
-  stagedMacAarch64Executable(files("$buildDir/executable/pkl-macos-aarch64"))
-  stagedLinuxAmd64Executable(files("$buildDir/executable/pkl-linux-amd64"))
-  stagedLinuxAarch64Executable(files("$buildDir/executable/pkl-linux-aarch64"))
-  stagedAlpineLinuxAmd64Executable(files("$buildDir/executable/pkl-alpine-linux-amd64"))
+  stagedMacAmd64Executable(files("build/executable/pkl-macos-amd64"))
+  stagedMacAarch64Executable(files("build/executable/pkl-macos-aarch64"))
+  stagedLinuxAmd64Executable(files("build/executable/pkl-linux-amd64"))
+  stagedLinuxAarch64Executable(files("build/executable/pkl-linux-aarch64"))
+  stagedAlpineLinuxAmd64Executable(files("build/executable/pkl-alpine-linux-amd64"))
 }
 
 tasks.jar {
@@ -90,7 +90,7 @@ tasks.shadowJar {
 
 val javaExecutable by tasks.registering(ExecutableJar::class) {
   inJar.set(tasks.shadowJar.flatMap { it.archiveFile })
-  outJar.set(file("$buildDir/executable/jpkl"))
+  outJar.set(file("build/executable/jpkl"))
 
   // uncomment for debugging
   //jvmArgs.addAll("-ea", "-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005")
@@ -117,7 +117,7 @@ tasks.check {
 // To catch this and similar problems, test that Java executable starts successfully.
 val testStartJavaExecutable by tasks.registering(Exec::class) {
   dependsOn(javaExecutable)
-val outputFile = file("$buildDir/testStartJavaExecutable") // dummy output to satisfy up-to-date check
+val outputFile = file("build/testStartJavaExecutable") // dummy output to satisfy up-to-date check
   outputs.file(outputFile)
   
   executable = javaExecutable.get().outputs.files.singleFile.toString()
@@ -209,7 +209,7 @@ fun Exec.configureExecutable(isEnabled: Boolean, outputFile: File, extraArgs: Li
  * Builds the pkl CLI for macOS/amd64.
  */
 val macExecutableAmd64: TaskProvider<Exec> by tasks.registering(Exec::class) {
-  configureExecutable(buildInfo.os.isMacOsX && buildInfo.graalVm.isGraal22, file("$buildDir/executable/pkl-macos-amd64"))
+  configureExecutable(buildInfo.os.isMacOsX && buildInfo.graalVm.isGraal22, file("build/executable/pkl-macos-amd64"))
 }
 
 /**
@@ -221,7 +221,7 @@ val macExecutableAmd64: TaskProvider<Exec> by tasks.registering(Exec::class) {
 val macExecutableAarch64: TaskProvider<Exec> by tasks.registering(Exec::class) {
   configureExecutable(
     buildInfo.os.isMacOsX && !buildInfo.graalVm.isGraal22,
-    file("$buildDir/executable/pkl-macos-aarch64"),
+    file("build/executable/pkl-macos-aarch64"),
     listOf(
       "--initialize-at-run-time=org.msgpack.core.buffer.DirectBufferAccess",
       "-H:+AllowDeprecatedBuilderClassesOnImageClasspath"
@@ -233,7 +233,7 @@ val macExecutableAarch64: TaskProvider<Exec> by tasks.registering(Exec::class) {
  * Builds the pkl CLI for linux/amd64.
  */
 val linuxExecutableAmd64: TaskProvider<Exec> by tasks.registering(Exec::class) {
-  configureExecutable(buildInfo.os.isLinux && buildInfo.arch == "amd64", file("$buildDir/executable/pkl-linux-amd64"))
+  configureExecutable(buildInfo.os.isLinux && buildInfo.arch == "amd64", file("build/executable/pkl-linux-amd64"))
 }
 
 /**
@@ -243,7 +243,7 @@ val linuxExecutableAmd64: TaskProvider<Exec> by tasks.registering(Exec::class) {
  * ARM instances.
  */
 val linuxExecutableAarch64: TaskProvider<Exec> by tasks.registering(Exec::class) {
-  configureExecutable(buildInfo.os.isLinux && buildInfo.arch == "aarch64", file("$buildDir/executable/pkl-linux-aarch64"))
+  configureExecutable(buildInfo.os.isLinux && buildInfo.arch == "aarch64", file("build/executable/pkl-linux-aarch64"))
 }
 
 /**
@@ -255,7 +255,7 @@ val linuxExecutableAarch64: TaskProvider<Exec> by tasks.registering(Exec::class)
 val alpineExecutableAmd64: TaskProvider<Exec> by tasks.registering(Exec::class) {
   configureExecutable(
       buildInfo.os.isLinux && buildInfo.arch == "amd64" && buildInfo.hasMuslToolchain,
-      file("$buildDir/executable/pkl-alpine-linux-amd64"),
+      file("build/executable/pkl-alpine-linux-amd64"),
       listOf(
         "--static",
         "--libc=musl",

pkl-cli/src/test/kotlin/org/pkl/cli/CliPackageDownloaderTest.kt

@@ -109,7 +109,7 @@ class CliPackageDownloaderTest {
         packageUris =
           listOf(
             PackageUri(
-              "package://localhost:12110/birds@0.5.0::sha256:3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "package://localhost:12110/birds@0.5.0::sha256:0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             ),
           ),
         noTransitive = true
@@ -140,7 +140,7 @@ class CliPackageDownloaderTest {
         """
       Cannot download package `package://localhost:12110/birds@0.5.0` because the computed checksum for package metadata does not match the expected checksum.
 
-      Computed checksum: "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+      Computed checksum: "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
       Expected checksum: "intentionallyBogusChecksum"
       Asset URL: "https://localhost:12110/birds@0.5.0"
     """
@@ -204,7 +204,7 @@ class CliPackageDownloaderTest {
         Failed to download package://localhost:12110/badChecksum@1.0.0 because:
         Cannot download package `package://localhost:12110/badChecksum@1.0.0` because the computed checksum does not match the expected checksum.
 
-        Computed checksum: "0ec8a501e974802d0b71b8d58141e1e6eaa10bc2033e18200be3a978823d98aa"
+        Computed checksum: "a6bf858cdd1c09da475c2abe50525902580910ee5cc1ff624999170591bf8f69"
         Expected checksum: "intentionally bogus checksum"
         Asset URL: "https://localhost:12110/badChecksum@1.0.0/badChecksum@1.0.0.zip"
 

pkl-cli/src/test/kotlin/org/pkl/cli/CliProjectPackagerTest.kt

@@ -248,7 +248,7 @@ class CliProjectPackagerTest {
               "type": "remote",
               "uri": "projectpackage://localhost:12110/fruit@1.0.5",
               "checksums": {
-                "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+                "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
               }
             }
           }
@@ -915,7 +915,7 @@ class CliProjectPackagerTest {
       Package `package://localhost:12110/birds@0.5.0` was already published with different contents.
       
       Computed checksum: 7324e17214b6dcda63ebfb57d5a29b077af785c13bed0dc22b5138628a3f8d8f
-      Published checksum: 3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118
+      Published checksum: 0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453
     """
           .trimIndent()
       )

pkl-cli/src/test/kotlin/org/pkl/cli/CliProjectResolverTest.kt

@@ -102,14 +102,14 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/birds@0.5.0",
             "checksums": {
-              "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "sha256": "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             }
           },
           "package://localhost:12110/fruit@1": {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.0.5",
             "checksums": {
-              "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+              "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
             }
           }
         }
@@ -157,14 +157,14 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/birds@0.5.0",
             "checksums": {
-              "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "sha256": "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             }
           },
           "package://localhost:12110/fruit@1": {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.0.5",
             "checksums": {
-              "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+              "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
             }
           }
         }
@@ -255,14 +255,14 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/birds@0.5.0",
             "checksums": {
-              "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "sha256": "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             }
           },
           "package://localhost:12110/fruit@1": {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.1.0",
             "checksums": {
-              "sha256": "98ad9fc407a79dc3fd5595e7a29c3803ade0a6957c18ec94b8a1624360b24f01"
+              "sha256": "a82e92e0c259591111d09d18a14f5ad66e2b6e13d827ee3e6f7ce06f5d0fbe0c"
             }
           },
           "package://localhost:12110/package2@5": {
@@ -337,14 +337,14 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/birds@0.5.0",
             "checksums": {
-              "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "sha256": "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             }
           },
           "package://localhost:12110/fruit@1": {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.0.5",
             "checksums": {
-              "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+              "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
             }
           }
         }
@@ -420,14 +420,14 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/birds@0.5.0",
             "checksums": {
-              "sha256": "3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118"
+              "sha256": "0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453"
             }
           },
           "package://localhost:12110/fruit@1": {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.0.5",
             "checksums": {
-              "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+              "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
             }
           }
         }
@@ -445,7 +445,7 @@ class CliProjectResolverTest {
             "type": "remote",
             "uri": "projectpackage://localhost:12110/fruit@1.1.0",
             "checksums": {
-              "sha256": "98ad9fc407a79dc3fd5595e7a29c3803ade0a6957c18ec94b8a1624360b24f01"
+              "sha256": "a82e92e0c259591111d09d18a14f5ad66e2b6e13d827ee3e6f7ce06f5d0fbe0c"
             }
           }
         }