Fix deprecation warnings in Gradle 4.8

[alpar-t]

The upgrade to Gradle 4.8 from #31230 come with some new deprecation warnings:

Creating a custom task named 'wrapper' has been deprecated and is scheduled to be removed in Gradle 5.0. You can configure the existing task using the 'wrapper { }' syntax or create your custom task under a different name.'.

As part of making the publishing plugins stable, the 'deferred configurable' behavior of the 'publishing {}' block is now deprecated. Please add 'enableFeaturePreview('STABLE_PUBLISHING')' to your settings file and do a test run by publishing to a local repository. If all artifacts are published as expected, there is nothing else to do. If the published artifacts change unexpectedly, please see the migration guide for more details: https://docs.gradle.org/4.8/userguide/publishing_maven.html#publishing_maven:deferred_configuration. In Gradle 5.0 the flag will be removed and the new behavior will become the default.

The AbstractFileCollection.getBuildDependencies() method has been deprecated and is scheduled to be removed in Gradle 5.0. Do not extend AbstractFileCollection, use Project.files() instead.
	at org.gradle.api.internal.file.AbstractFileCollection.getBuildDependencies(AbstractFileCollection.java:209)
	at org.gradle.api.internal.tasks.CachingTaskDependencyResolveContext$TaskGraphImpl.getNodeValues(CachingTaskDependencyResolveContext.java:93)
	at org.gradle.internal.graph.CachingDirectedGraphWalker$GraphWithEmpyEdges.getNodeValues(CachingDirectedGraphWalker.java:211)
	at org.gradle.internal.graph.CachingDirectedGraphWalker.doSearch(CachingDirectedGraphWalker.java:121)
	at org.gradle.internal.graph.CachingDirectedGraphWalker.findValues(CachingDirectedGraphWalker.java:73)
	at org.gradle.api.internal.tasks.CachingTaskDependencyResolveContext.doGetDependencies(CachingTaskDependencyResolveContext.java:76)
	at org.gradle.api.internal.tasks.CachingTaskDependencyResolveContext.getDependencies(CachingTaskDependencyResolveContext.java:60)

[elasticmachine]

Pinging @elastic/es-core-infra

[jasontedor]

Relates #31230

[alpar-t]

the last one around AbstractFileCollection seems to be gralde relatet, but as gradle/gradle#5141 explains it has to do with GradleUp/shadow#370. It's fixed by moving to version 2.0.4 of the plugin.