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Change APM Server example settings used in E2E testing #5094

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We should change those two particular settings as they are being deprecated and cause the below.

{"log.level":"warn","@timestamp":"2021-11-24T02:20:33.480Z","log.logger":"index-management","log.origin":{"file.name":"idxmgmt/supporter_factory.go","file.line":159},"message":"deprecated config `apm-server.ilm` specified. This config will be removed in 8.0.","service.name":"apm-server","ecs.version":"1.6.0"}
{"log.level":"warn","@timestamp":"2021-11-24T02:06:20.813Z","log.logger":"index-management","log.origin":{"file.name":"idxmgmt/supporter_factory.go","file.line":156},"message":"deprecated config `setup.template` specified. This config will be removed in 8.0.","service.name":"apm-server","ecs.version":"1.6.0"}
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