Add ability to specify capabilities in setup

[ejizba]

and clarify that setup options are merged instead of replaced. Otherwise there would be no way for multiple places (i.e. the user's app and an otel package) to adjust setup config.

Related to otel work #245, we will need to do something like this:

app.setup({
    capabilities: {
        WorkerOpenTelemetryEnabled: true,
    },
});