* Remove nonexistent paths from our API tests config

These paths (or rather their absence) breaks the functional_tests_server script.

An analogous problem for cases was fixed in elastic#79127.

* Remove duplicated context from logger

This context is already provided to the logger by kibana; adding it a
second time leads to duplicated log tags, e.g.:

```
server    log   [12:36:07.138] [debug][plugins][plugins][securitySolution][securitySolution] ...
```

This is now fixed:

```
server    log   [12:41:52.112] [debug][plugins][securitySolution] ...
```