Update dependencies (apple#689)

- Update dependencies by deleting lock files and regenerating them with `gw updateDependencyLocks`.
  Deleting lock files avoids strange `some.library:some.older.version=default` entries.
  Most updated dependencies are test dependencies.
- Handle breaking changes in library commonmark.
- Fix test to close PackageServer exactly once.
  This problem surfaced because JUnit 5.11 changed override rules for lifecycle methods,
  resulting in too many instead of too few close() calls.
- Bump msgpack version
- Bump clikt version
- Bump Gradle plugin versions

bench/gradle.lockfile

@@ -2,12 +2,12 @@
 # Manual edits can break the build and are not advised.
 # This file is expected to be part of source control.
 com.tunnelvisionlabs:antlr4-runtime:4.9.0=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
-net.bytebuddy:byte-buddy:1.14.16=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+net.bytebuddy:byte-buddy:1.14.18=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 net.java.dev.jna:jna:5.6.0=kotlinCompilerClasspath,kotlinKlibCommonizerClasspath
 net.sf.jopt-simple:jopt-simple:5.0.4=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
 org.apache.commons:commons-math3:3.6.1=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
 org.apiguardian:apiguardian-api:1.1.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeOnlyDependenciesMetadata
-org.assertj:assertj-core:3.26.0=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+org.assertj:assertj-core:3.26.3=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.graalvm.compiler:compiler:23.0.2=graal
 org.graalvm.sdk:graal-sdk:23.0.2=graal,jmh,jmhRuntimeClasspath,truffle
 org.graalvm.truffle:truffle-api:23.0.2=graal,jmh,jmhRuntimeClasspath,truffle
@@ -26,12 +26,12 @@ org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.7.10=testCompileClasspath,testImplemen
 org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.7.10=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.jetbrains.kotlin:kotlin-stdlib:1.7.10=kotlinCompilerClasspath,kotlinCompilerPluginClasspathJmh,kotlinCompilerPluginClasspathMain,kotlinCompilerPluginClasspathTest,kotlinKlibCommonizerClasspath,testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.jetbrains:annotations:13.0=kotlinCompilerClasspath,kotlinCompilerPluginClasspathJmh,kotlinCompilerPluginClasspathMain,kotlinCompilerPluginClasspathTest,kotlinKlibCommonizerClasspath,testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
-org.junit.jupiter:junit-jupiter-api:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.jupiter:junit-jupiter-engine:5.10.2=testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.jupiter:junit-jupiter-params:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
-org.junit.platform:junit-platform-commons:1.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.platform:junit-platform-engine:1.10.2=testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit:junit-bom:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-api:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-engine:5.11.2=testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-params:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+org.junit.platform:junit-platform-commons:1.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.platform:junit-platform-engine:1.11.2=testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit:junit-bom:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
 org.openjdk.jmh:jmh-core:1.37=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
 org.openjdk.jmh:jmh-generator-asm:1.37=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
 org.openjdk.jmh:jmh-generator-bytecode:1.37=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
@@ -40,4 +40,4 @@ org.opentest4j:opentest4j:1.3.0=testCompileClasspath,testImplementationDependenc
 org.organicdesign:Paguro:3.10.3=jmh,jmhRuntimeClasspath
 org.ow2.asm:asm:9.0=jmh,jmhCompileClasspath,jmhImplementationDependenciesMetadata,jmhRuntimeClasspath
 org.snakeyaml:snakeyaml-engine:2.5=jmh,jmhRuntimeClasspath
-empty=annotationProcessor,apiDependenciesMetadata,archives,compile,compileClasspath,compileOnly,compileOnlyDependenciesMetadata,default,implementationDependenciesMetadata,intransitiveDependenciesMetadata,jmhAnnotationProcessor,jmhApiDependenciesMetadata,jmhCompile,jmhCompileOnly,jmhCompileOnlyDependenciesMetadata,jmhIntransitiveDependenciesMetadata,jmhKotlinScriptDef,jmhKotlinScriptDefExtensions,jmhRuntime,jmhRuntimeOnlyDependenciesMetadata,kotlinCompilerPluginClasspath,kotlinNativeCompilerPluginClasspath,kotlinScriptDef,kotlinScriptDefExtensions,runtime,runtimeClasspath,runtimeOnlyDependenciesMetadata,sourcesJar,testAnnotationProcessor,testApiDependenciesMetadata,testCompile,testCompileOnly,testCompileOnlyDependenciesMetadata,testIntransitiveDependenciesMetadata,testKotlinScriptDef,testKotlinScriptDefExtensions,testRuntime
+empty=annotationProcessor,apiDependenciesMetadata,compileClasspath,compileOnlyDependenciesMetadata,implementationDependenciesMetadata,intransitiveDependenciesMetadata,jmhAnnotationProcessor,jmhApiDependenciesMetadata,jmhCompileOnlyDependenciesMetadata,jmhIntransitiveDependenciesMetadata,jmhKotlinScriptDef,jmhKotlinScriptDefExtensions,jmhRuntimeOnlyDependenciesMetadata,kotlinCompilerPluginClasspath,kotlinNativeCompilerPluginClasspath,kotlinScriptDef,kotlinScriptDefExtensions,runtimeClasspath,runtimeOnlyDependenciesMetadata,sourcesJar,testAnnotationProcessor,testApiDependenciesMetadata,testCompileOnlyDependenciesMetadata,testIntransitiveDependenciesMetadata,testKotlinScriptDef,testKotlinScriptDefExtensions

docs/gradle.lockfile

@@ -2,11 +2,11 @@
 # Manual edits can break the build and are not advised.
 # This file is expected to be part of source control.
 com.tunnelvisionlabs:antlr4-runtime:4.9.0=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
-io.leangen.geantyref:geantyref:1.3.15=testRuntimeClasspath
-net.bytebuddy:byte-buddy:1.14.16=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+io.leangen.geantyref:geantyref:1.3.16=testRuntimeClasspath
+net.bytebuddy:byte-buddy:1.14.18=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 net.java.dev.jna:jna:5.6.0=kotlinCompilerClasspath,kotlinKlibCommonizerClasspath
 org.apiguardian:apiguardian-api:1.1.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeOnlyDependenciesMetadata
-org.assertj:assertj-core:3.26.0=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+org.assertj:assertj-core:3.26.3=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.graalvm.sdk:graal-sdk:23.0.2=testRuntimeClasspath
 org.graalvm.truffle:truffle-api:23.0.2=testRuntimeClasspath
 org.jetbrains.intellij.deps:trove4j:1.0.20200330=kotlinCompilerClasspath,kotlinKlibCommonizerClasspath
@@ -24,13 +24,13 @@ org.jetbrains.kotlin:kotlin-stdlib-jdk7:1.7.10=testCompileClasspath,testImplemen
 org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.7.10=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.jetbrains.kotlin:kotlin-stdlib:1.7.10=kotlinCompilerClasspath,kotlinCompilerPluginClasspathMain,kotlinCompilerPluginClasspathTest,kotlinKlibCommonizerClasspath,testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
 org.jetbrains:annotations:13.0=kotlinCompilerClasspath,kotlinCompilerPluginClasspathMain,kotlinCompilerPluginClasspathTest,kotlinKlibCommonizerClasspath,testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
-org.junit.jupiter:junit-jupiter-api:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.jupiter:junit-jupiter-engine:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.jupiter:junit-jupiter-params:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
-org.junit.platform:junit-platform-commons:1.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit.platform:junit-platform-engine:1.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
-org.junit:junit-bom:5.10.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-api:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-engine:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.jupiter:junit-jupiter-params:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath
+org.junit.platform:junit-platform-commons:1.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit.platform:junit-platform-engine:1.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
+org.junit:junit-bom:5.11.2=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
 org.opentest4j:opentest4j:1.3.0=testCompileClasspath,testImplementationDependenciesMetadata,testRuntimeClasspath,testRuntimeOnlyDependenciesMetadata
 org.organicdesign:Paguro:3.10.3=testRuntimeClasspath
 org.snakeyaml:snakeyaml-engine:2.5=testRuntimeClasspath
-empty=annotationProcessor,apiDependenciesMetadata,archives,compile,compileClasspath,compileOnly,compileOnlyDependenciesMetadata,default,implementationDependenciesMetadata,intransitiveDependenciesMetadata,kotlinCompilerPluginClasspath,kotlinNativeCompilerPluginClasspath,kotlinScriptDef,kotlinScriptDefExtensions,runtime,runtimeClasspath,runtimeOnlyDependenciesMetadata,testAnnotationProcessor,testApiDependenciesMetadata,testCompile,testCompileOnly,testCompileOnlyDependenciesMetadata,testIntransitiveDependenciesMetadata,testKotlinScriptDef,testKotlinScriptDefExtensions,testRuntime
+empty=annotationProcessor,apiDependenciesMetadata,compileClasspath,compileOnlyDependenciesMetadata,implementationDependenciesMetadata,intransitiveDependenciesMetadata,kotlinCompilerPluginClasspath,kotlinNativeCompilerPluginClasspath,kotlinScriptDef,kotlinScriptDefExtensions,runtimeClasspath,runtimeOnlyDependenciesMetadata,testAnnotationProcessor,testApiDependenciesMetadata,testCompileOnlyDependenciesMetadata,testIntransitiveDependenciesMetadata,testKotlinScriptDef,testKotlinScriptDefExtensions

gradle/libs.versions.toml

@@ -1,8 +1,8 @@
 [versions] # ordered alphabetically
 antlr = "4.+"
 assertj = "3.+" 
-checksumPlugin = "1.2.0"
-clikt = "3.5.1"
+checksumPlugin = "1.4.0"
+clikt = "3.+"
 commonMark = "0.+"
 downloadTaskPlugin = "5.6.0"
 geantyref = "1.+"
@@ -16,15 +16,16 @@ graalVmSha256-macos-aarch64 = "e944c5ce5da56e683fc8f1a57191b46d9cb702930b1688bda
 graalVmSha256-linux-x64 = "112dc9b92d81a946f1b5b334646151b790785c813e76fcf13527a319003d7e2c"
 graalVmSha256-linux-aarch64 = "c95ac550d070f06666cf8c1023a098380dd565be00866473caf6ff1b7cdf680c"
 graalVmSha256-windows-x64 = "1ab2291e71f54d73e3e57b7fccbf184cabcba37e16ca9d1cf42d08474a7c02f0"
-ideaExtPlugin = "1.1"
+ideaExtPlugin = "1.1.9"
 javaPoet = "1.+"
 javaxInject = "1"
 jansi = "2.+"
 jimfs = "1.+"
-# 3.25.1 doesn't work with native image
+# later versions don't work with native image
+# (at least not without additional configuration; tested with 3.25.1 and 3.27.1)
 jline = "3.23.0"
 jmh = "1.+"
-jmhPlugin = "0.6.6"
+jmhPlugin = "0.7.2"
 jsr305 = "3.+"
 junit = "5.+"
 kotlin = "1.7.10"
@@ -38,15 +39,16 @@ ktfmt = "0.44"
 # replaces nuValidator's log4j dependency
 # something related to log4j-1.2-api is apparently broken in 2.17.2
 log4j = "2.17.1"
-msgpack = "0.9.0"
-nexusPublishPlugin = "1.3.0"
+msgpack = "0.9.8"
+nexusPublishPlugin = "2.0.0"
 nuValidator = "20.+"
 paguro = "3.+"
 shadowPlugin = "8.1.1"
 slf4j = "1.+"
-# Breaking change in snakeYaml 2.6 (removing DumpSettingsBuilder::setScalarResolver), so pin to 2.5
+# snakeYaml 2.6 removed DumpSettingsBuilder::setScalarResolver,
+# which is used by the external YAML renderer (org.pkl.core.YamlRenderer)
 snakeYaml = "2.5"
-spotlessPlugin = "6.11.0"
+spotlessPlugin = "6.25.0"
 wiremock = "3.+"
 
 [libraries] # ordered alphabetically