Solve Gradle deprecation warnings around shadowJar (#30483)

* Solve Gradle deprecation warnings around shadowJar

- Apply workaround for: johnrengelman/shadow#336
- bump plugin to 2.0.4

Changes between 2.0.2 and 2.0.4 of the plugin:
```
477db40 12 days ago john.engelman@target.com Release 2.0.4
3e3da37 3 weeks ago john.engelman@target.com Remove internal Gradle API and annotation internal getters on shadow jar.
31e2380 3 weeks ago john.engelman@target.com Close input streams. Closes #364
f712cc8 3 weeks ago john.engelman@target.com Upgrade ASM to 6.1.1 to address perf issues. Closes #374
2f94b2b 3 weeks ago john.engelman@target.com next version
23bbf3d 7 weeks ago john.r.engelman@gmail.com Add some gradle versions. Update changelog for 2.0.3
7435c74 7 weeks ago john.r.engelman@gmail.com Merge pull request #367 from ttsiebzehntt/366-java10
325c002 7 weeks ago info@martinsadowski.de Update ASM to 6.1
94550e5 3 months ago john.r.engelman@gmail.com Merge pull request #356 from sgnewson/update-file-to-files
66b691e 4 months ago john.r.engelman@gmail.com Merge pull request #358 from 3flex/patch-1
14761b1 4 months ago 3flex@users.noreply.github.com fix markdown for User Guide URL in issue template
a3f6984 4 months ago newson@synopsys.com update inputs.file to inputs.files, to remove warning
```

closes #30389

* Improove comment as suggested

benchmarks/build.gradle

@@ -24,22 +24,22 @@ buildscript {
         }
     }
     dependencies {
-        classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.2'
+        classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
     }
 }
 
 apply plugin: 'elasticsearch.build'
-// build an uberjar with all benchmarks
-apply plugin: 'com.github.johnrengelman.shadow'
-// have the shadow plugin provide the runShadow task
-apply plugin: 'application'
+
+// order of this seciont matters, see: https://github.com/johnrengelman/shadow/issues/336
+apply plugin: 'application' // have the shadow plugin provide the runShadow task
+mainClassName = 'org.openjdk.jmh.Main'
+apply plugin: 'com.github.johnrengelman.shadow' // build an uberjar with all benchmarks
 
 // Not published so no need to assemble
 tasks.remove(assemble)
 build.dependsOn.remove('assemble')
 
 archivesBaseName = 'elasticsearch-benchmarks'
-mainClassName = 'org.openjdk.jmh.Main'
 
 test.enabled = false