Multi-index query CLI support

[KennyZhang1]

Description

This PR modifies the GraphRagConfig object to support multi-index querying at the CLI-layer.

Related Issues

This PR builds on top of a previous PR that supports multi-index querying in the API layer: #1644

Proposed Changes

• Modify the "Output" section of the GraphRagConfig to support passing in a dict of OutputConfigs used to represent the location of multiple indexes.
• Refactor the query CLI layer to support new output config structure and provide appropriate connections to multi-index query API functions
• Modify all test code to reflect changes to the GraphRagConfig output structure.

Checklist

• I have tested these changes locally.
• I have reviewed the code changes.
• I have updated the documentation (if necessary).
• I have added appropriate unit tests (if applicable).

Additional Notes

N/A