[Agent] The agent doesn't correctly merges items at the input level with and the stream level.

[ph]

With the following defined datasource, I believe the problem is in the way we merge the configuration at the datasource's input level and the stream level to generate the metricbeat's input configuration.

datasources:
  - namespace: default
    enabled: true
    use_output: default
    inputs:
      - type: nginx/metrics
        enabled: true
        streams:
          - enabled: true
            dataset: nginx.stubstatus
            period: 10s
            id: nginx/metrics-nginx.stubstatus
        hosts:
          - 'http://127.0.0.1:8080'

Results in the metricbeat logs

2020-03-31T15:54:06.298-0400	INFO	instance/beat.go:609	Home path: [/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64] Config path: [/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64] Data path: [/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/default/metricbeat--8.0.0] Logs path: [/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64/logs]
2020-03-31T15:54:06.339-0400	INFO	instance/beat.go:617	Beat ID: 36f61016-0809-44a5-a30c-184411bea2a0
2020-03-31T15:54:06.340-0400	INFO	[centralmgmt.fleet]	fleet/manager.go:272	initiating fleet config manager
2020-03-31T15:54:06.413-0400	INFO	[beat]	instance/beat.go:945	Beat info	{"system_info": {"beat": {"path": {"config": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64", "data": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/default/metricbeat--8.0.0", "home": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64", "logs": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64/logs"}, "type": "metricbeat", "uuid": "36f61016-0809-44a5-a30c-184411bea2a0"}}}
2020-03-31T15:54:06.413-0400	INFO	[beat]	instance/beat.go:954	Build info	{"system_info": {"build": {"commit": "unknown", "libbeat": "8.0.0", "time": "1754-08-30T22:43:41.128Z", "version": "8.0.0"}}}
2020-03-31T15:54:06.413-0400	INFO	[beat]	instance/beat.go:957	Go runtime info	{"system_info": {"go": {"os":"darwin","arch":"amd64","max_procs":16,"version":"go1.13.8"}}}
2020-03-31T15:54:06.445-0400	INFO	[beat]	instance/beat.go:961	Host info	{"system_info": {"host": {"architecture":"x86_64","boot_time":"2020-03-31T11:01:44.826172-04:00","name":"Nicolass-MacBook-Pro.local","ip":["127.0.0.1/8","::1/128","fe80::1/64","fe80::aede:48ff:fe00:1122/64","fe80::c10:40a7:fb66:b576/64","192.168.0.10/24","fd00:688f:2ed3:7dd2:10a7:a049:d3f0:2787/64","fd00:688f:2ed3:7dd2:7158:416f:330f:58cc/64","fe80::444c:ff:fede:3ef5/64","fe80::444c:ff:fede:3ef5/64","fe80::e2df:ea9f:b034:ac0/64","fe80::1f2f:614d:8ff0:8e53/64","fe80::353a:ba8f:803d:1038/64","fe80::caae:2fa0:7559:3e79/64"],"kernel_version":"19.4.0","mac":["ac:de:48:00:11:22","82:46:af:c6:8c:01","a6:83:e7:4e:a2:42","a4:83:e7:4e:a2:42","82:46:af:c6:8c:00","82:46:af:c6:8c:01","82:46:af:c6:8c:05","82:46:af:c6:8c:04","06:83:e7:4e:a2:42","46:4c:00:de:3e:f5","46:4c:00:de:3e:f5"],"os":{"family":"darwin","platform":"darwin","name":"Mac OS X","version":"10.15.4","major":10,"minor":15,"patch":4,"build":"19E266"},"timezone":"EDT","timezone_offset_sec":-14400,"id":"A4D26E5E-1CCB-57BF-8AB6-39A955488947"}}}
2020-03-31T15:54:06.450-0400	INFO	[beat]	instance/beat.go:990	Process info	{"system_info": {"process": {"cwd": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64", "exe": "/Users/nicolas/go/src/github.com/elastic/beats/x-pack/agent/build/distributions/agent-8.0.0-darwin-x86_64/data/install/metricbeat-8.0.0-darwin-x86_64/metricbeat", "name": "metricbeat", "pid": 89800, "ppid": 89610, "start_time": "2020-03-31T15:54:05.343-0400"}}}
2020-03-31T15:54:06.460-0400	INFO	instance/beat.go:296	Setup Beat: metricbeat; Version: 8.0.0
2020-03-31T15:54:06.471-0400	INFO	eslegclient/connection.go:84	elasticsearch url: http://localhost:9200
2020-03-31T15:54:06.482-0400	INFO	[publisher]	pipeline/module.go:110	Beat name: Nicolass-MacBook-Pro.local
2020-03-31T15:54:06.495-0400	INFO	[monitoring]	log/log.go:118	Starting metrics logging every 30s
2020-03-31T15:54:06.495-0400	INFO	instance/beat.go:437	metricbeat start running.
2020-03-31T15:54:06.509-0400	WARN	[cfgwarn]	fleet/manager.go:105	BETA: Fleet management is enabled
2020-03-31T15:54:06.509-0400	INFO	[centralmgmt.fleet]	fleet/manager.go:106	Starting fleet management service
2020-03-31T15:54:06.510-0400	INFO	cfgfile/reload.go:175	Config reloader started
2020-03-31T15:54:06.528-0400	INFO	cfgfile/reload.go:235	Loading of config files completed.
2020-03-31T15:54:07.067-0400	INFO	[centralmgmt.fleet]	fleet/manager.go:190	Applying settings for metricbeat.modules
2020-03-31T15:54:07.071-0400	ERROR	[centralmgmt]	cfgfile/list.go:96	Error creating runner from config: 1 error: host parsing failed for nginx-stubstatus: error parsing URL: empty host
2020-03-31T15:54:07.079-0400	ERROR	[centralmgmt.fleet]	fleet/manager.go:226	1 error: Error creating runner from config: 1 error: host parsing failed for nginx-stubstatus: error parsing URL: empty host
2020-03-31T15:54:07.089-0400	INFO	[centralmgmt.fleet]	fleet/manager.go:190	Applying settings for output
2020-03-31T15:54:07.089-0400	INFO	eslegclient/connection.go:84	elasticsearch url: http://localhost:9200
2020-03-31T15:54:07.099-0400	ERROR	[centralmgmt.fleet]	fleet/manager.go:147	Could not apply the configuration, error: [1 error: Error creating runner from config: 1 error: host parsing failed for nginx-stubstatus: error parsing URL: empty host]
2020-03-31T15:54:09.342-0400	INFO	[add_cloud_metadata]	add_cloud_metadata/add_cloud_metadata.go:89	add_cloud_metadata: hosting provider type not detected.
2020-03-31T15:54:10.346-0400	INFO	[publisher_pipeline_output]	pipeline/output.go:101	Connecting to backoff(elasticsearch(http://localhost:9200))
2020-03-31T15:54:10.349-0400	INFO	[esclientleg]	eslegclient/connection.go:263	Attempting to connect to Elasticsearch version 8.0.0-SNAPSHOT
2020-03-31T15:54:10.381-0400	INFO	[license]	licenser/check.go:35	License is active for Basic
2020-03-31T15:54:10.411-0400	INFO	[license]	licenser/check.go:22	Trial license active
2020-03-31T15:54:10.411-0400	INFO	[license]	licenser/es_callback.go:51	Elasticsearch license: Trial
``

[elasticmachine]

Pinging @elastic/ingest-management (Team:Ingest Management)