Remove deprecated --setup, --version, and --configflags CLI flags

[urso]

Remove flags and references from:

• libbeat/cmd/instance
• tests
• Beats Documentation

[kvch]

The package libbeat still contains a reference to -setup flag in libbeat/_meta/config.yml under the dashboards section:

Loading the dashboards is disabled by default and can be enabled either by setting the
options here, or by using the -setup CLI flag or the setup command.

I have found a few instaces of -configtest in the folllowing E2E tests:

• packetbeat/tests/system/test_0026_test_config.py
• winlogbeat/tests/system/test_config.py
• winlogbeat/tests/system/test_eventlogging.py
• winlogbeat/tests/system/test_wineventlog.py

Nit: One more comment referring to -version in libbeat/cmd/instace/beat.go:

 // handleFlags parses the command line flags. It handles the '-version' flag
// and invokes the HandleFlags callback if implemented by the Beat.
func (b *Beat) handleFlags() error {

[urso]

@kvch Thanks. These settings are everywhere :)

[urso]

beats-ci is acting up once again :(

Travis is green + related windows tests have been green as well: https://beats-ci.elastic.co/job/elastic+beats+pull-request+multijob-windows/beat=winlogbeat,label=windows/3948/console

[urso]

Jenkins, test this.

[dedemorton]

Also remove the sentence on line 571/572 that says: "Use this command instead of run --setup when you want to set up the environment without actually running {beatname_uc} and ingesting data.

[urso]

Thanks. I modified the sentence to:

Use this command if you want to set up the environment without actually running
{beatname_uc} and ingesting data.

[dedemorton]

Doc changes LGTM