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-doc/src/test/files/DocGeneratorTest/output/localhost:12110/birds/0.5.0/index.html

@@ -39,7 +39,7 @@
           <dt class="">Dependencies:</dt>
           <dd><a href="https://example.com/fruit-docs">fruit:1.0.5</a>, <a href="https://pages.github.com/apple/pkl/stdlib/pkl/0.24.0/">pkl:0.24.0</a></dd>
           <dt class="">Checksum:</dt>
-          <dd>3f19ab9fcee2f44f93a75a09e531db278c6d2cd25206836c8c2c4071cd7d3118</dd>
+          <dd>0a5ad2dc13f06f73f96ba94e8d01d48252bc934e2de71a837620ca0fef8a7453</dd>
           <dt class="runtime-data hidden">Known usages:</dt>
           <dd id="known-usages" class="runtime-data hidden"></dd>
           <dt class="runtime-data hidden">All versions:</dt>

pkl-doc/src/test/files/DocGeneratorTest/output/localhost:12110/fruit/1.1.0/index.html

@@ -39,7 +39,7 @@
           <dt class="">Dependencies:</dt>
           <dd><a href="https://pages.github.com/apple/pkl/stdlib/pkl/0.24.0/">pkl:0.24.0</a></dd>
           <dt class="">Checksum:</dt>
-          <dd>98ad9fc407a79dc3fd5595e7a29c3803ade0a6957c18ec94b8a1624360b24f01</dd>
+          <dd>a82e92e0c259591111d09d18a14f5ad66e2b6e13d827ee3e6f7ce06f5d0fbe0c</dd>
           <dt class="runtime-data hidden">Known usages:</dt>
           <dd id="known-usages" class="runtime-data hidden"></dd>
           <dt class="runtime-data hidden">All versions:</dt>