[Gradle] Cleanup test mutes for gradle func tests (elastic#133768) (elastic#133787)

(cherry picked from commit 4a745b5)

# Conflicts:
#	muted-tests.yml

Author: breskeby

muted-tests.yml

@@ -534,18 +534,9 @@ tests:
 - class: org.elasticsearch.packaging.test.DebPreservationTests
   method: test40RestartOnUpgrade
   issue: https://github.com/elastic/elasticsearch/issues/125821
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionManagementPluginFuncTest
-  method: cannot change committed ids to a branch
-  issue: https://github.com/elastic/elasticsearch/issues/132790
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionManagementPluginFuncTest
-  method: latest files cannot change base id
-  issue: https://github.com/elastic/elasticsearch/issues/132789
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionManagementPluginFuncTest
-  method: definitions have primary ids which cannot change
-  issue: https://github.com/elastic/elasticsearch/issues/132788
 - class: org.elasticsearch.core.GlobTests
   method: testSuffixMatch
   issue: https://github.com/elastic/elasticsearch/issues/133117
 - class: org.elasticsearch.smoketest.DocsClientYamlTestSuiteIT
   method: test {yaml=reference/snapshot-restore/apis/delete-snapshot-api/line_78}
-  issue: https://github.com/elastic/elasticsearch/issues/133438
+  issue: https://github.com/elastic/elasticsearch/issues/133438