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-core/src/test/files/LanguageSnippetTests/input/projects/project4/PklProject.deps.json

@@ -5,7 +5,7 @@
       "type": "remote",
       "uri": "projectpackage://localhost:12110/fruit@1.0.5",
       "checksums": {
-        "sha256": "b4ea243de781feeab7921227591e6584db5d0673340f30fab2ffe8ad5c9f75f5"
+        "sha256": "abd173e8a25f5b930b0e34269a441e32c9d95e0b0a715bc6eff918f0afd0688e"
       }
     }
   }