Prune controller-protocol.version from -deps bundle

[edsavage]

Summary

Follow-up fix to #3224. That PR added the controller-protocol.version marker to the -nodeps bundle's include list in create_dra.sh, but did not add it to the -deps bundle's prune list. Because the -deps zip is built as "everything not pruned", the marker leaked into both the -deps and -nodeps bundles.

Elasticsearch's ml plugin resolves both bundles and unzips them together into a single plugin bundle:

nativeBundle("org.elasticsearch.ml:ml-cpp:${mlCppVersion()}:deps@zip")   { changing = true }
nativeBundle("org.elasticsearch.ml:ml-cpp:${mlCppVersion()}:nodeps@zip") { changing = true }
// ...
esplugin.bundleSpec.from { configurations.nativeBundle.files.collect { zipTree(it) } }

With the marker now present at the root of both zips, Gradle's Copy task hits a duplicate path and fails (there is no duplicatesStrategy set):

> Task :x-pack:plugin:ml:explodedBundlePlugin FAILED
Caused by: org.gradle.api.InvalidUserCodeException: Entry controller-protocol.version is a duplicate
but no duplicate handling strategy has been set.

This breaks Elasticsearch's :x-pack:plugin:ml:explodedBundlePlugin / bundlePlugin (and every downstream task that depends on them — bundle, release-tests, bwc-snapshots) on main and all open PRs once they resolve the post-#3224 snapshot.

Change

Add -path "**/controller-protocol.version" to the -deps bundle's -prune list so the marker ships only in -nodeps (where verifyControllerProtocolVersion expects it), and not in -deps. The marker is not a 3rd-party dependency, so it does not belong in the deps bundle regardless.

Testing

• -nodeps bundle still contains controller-protocol.version (unchanged include list).
• -deps bundle no longer contains it (now pruned), so the Elasticsearch bundle merge sees a single entry.

[elasticsearchmachine]

Pinging @elastic/ml-core (Team:ML)