Lint: Detect broken input definitions

There's a few input-related mistakes that can be introduced to a package and are difficult to spot, which will currently cause all checks/tests to pass but can cause an error when accessing package config in Kibana/Fleet (see https://github.com/elastic/kibana/issues/100340).

These mistakes are:
- Main `manifest.yml` defines an input that is not defined in any individual data_stream' `manifest.yml` (why this duplication in the first place?).
- `data_stream/x/manifest.yml` defines an input that is not defined in the main `manifest.yml`.
- `data_stream/x/manifest.yml` defines an input that links to an agent stream template file that doesn't exists.