[Bug]: index update does not process deleted documents

[mmaitre314]

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• I have searched the existing issues and this bug is not already filed.
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Describe the bug

Two issues related to handling deleted documents during index updates:

The code here fails if there are only documents to delete and no documents to add:

# Fail on empty delta dataset
if delta_dataset.new_inputs.empty:
    error_msg = "Incremental Indexing Error: No new documents to process."
    raise ValueError(error_msg)

graphrag/graphrag/index/run/run_workflows.py

Line 93 in 63042d2

if delta_dataset.new_inputs.empty:

(related to #1600)

In the same function, delta_dataset.deleted_inputs is not referenced and only delta_dataset.new_inputs is. So it looks like document deletion is not implemented. If that's the case, with some guidance I may be able to provide a PR.

Steps to reproduce

Run an index update with only documents to delete and no documents to add.

Expected Behavior

Updates containing only document deletions succeed and deleted documents are removed from the index.

GraphRAG Config Used

N/A

Logs and screenshots

No response

Additional Information

• GraphRAG Version: 1.1.2
• Operating System: Windows 11
• Python Version: 12
• Related Issues: graphrag CLI Update command issue #1600