docs: Document pattern for using non-exposed stream definitions as parent streams

## Summary

When building complex connectors with multi-level substream hierarchies, it's useful to define stream definitions that are only used internally as parent streams for other streams, without exposing them as top-level streams. This pattern is currently undocumented but is actively used in production connectors.

## Problem

The current YAML Reference documentation explains that only entries in the top-level `streams:` array are exposed as runnable streams, but it doesn't explicitly document the pattern of:
1. Defining a full stream definition in `definitions` that is NOT listed in `streams:`
2. Using that definition solely as a `parent_stream_config` for another stream
3. The naming convention some connectors use (e.g., `__` prefix) to signal "internal helper"

This pattern is particularly useful for 3-level nested substream hierarchies where an intermediate stream is needed to provide partition keys but shouldn't be exposed to users.

## Example Implementation: Jira Connector

The Jira connector uses this pattern extensively. Here are code permalinks:

### Internal/Private Stream Definitions (in `definitions`, NOT in `streams:`)

- [`__issue_property_keys_substream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L10055) - Used as parent for `issue_properties_stream`
- [`__custom_issue_fields_substream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L9882) - Used as parent for `issue_custom_field_contexts`
- [`__issue_custom_field_contexts_substream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L9971) - Used as parent for `issue_custom_field_options`
- [`__boards_substream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L11744) - Used as parent for board-related streams
- [`__story_points_issue_fields_substream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L13990) - Used for story points configuration

### How It's Used (3-level hierarchy example)

The [`issue_properties_stream`](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L10080-L10090) references the internal `__issue_property_keys_substream` as its parent:

```yaml
issue_properties_stream:
# ...
retriever:
# ...
partition_router:
type: SubstreamPartitionRouter
parent_stream_configs:
- type: ParentStreamConfig
stream: "#/definitions/__issue_property_keys_substream" # <-- Internal stream reference
```

This creates a 3-level hierarchy:
1. `issues_stream` (grandparent - exposed)
2. `__issue_property_keys_substream` (parent - internal, NOT exposed)
3. `issue_properties_stream` (child - exposed)

### Top-level `streams:` Section

The [streams section](https://github.com/airbytehq/airbyte/blob/b4a7fe87016dd6e12688d82545809696b0292055/airbyte-integrations/connectors/source-jira/manifest.yaml#L14555) only lists the streams that should be exposed to users - the `__`-prefixed definitions are intentionally omitted.

## Suggested Documentation

Add a section to the YAML Reference or a new "Advanced Patterns" page that documents:

1. **Pattern**: Using stream definitions as internal parent streams
2. **Use case**: Multi-level substream hierarchies where intermediate streams shouldn't be exposed
3. **Naming convention**: The `__` prefix convention (optional but recommended for clarity)
4. **Behavior**: Streams not listed in `streams:` will not be exposed by `source.streams(config)` - attempting to sync them will silently no-op
5. **Testing implications**: When writing mock server tests, always verify stream names against the `streams:` section to avoid testing non-existent streams

## Context

This issue was discovered while creating comprehensive mock server tests for the Jira connector (airbytehq/airbyte#70884). The pattern caused confusion when attempting to test `issue_property_keys` as a stream, only to discover it's an internal-only definition.

---
**Requested by:** AJ Steers (@aaronsteers)
**Related PR:** https://github.com/airbytehq/airbyte/pull/70884
**Devin session:** https://app.devin.ai/sessions/f152f435f9d146688e476611ff864c30