Update dependencies (#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

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