fix(index): warn when skipping failed documents

[Iams4kura]

Summary

• Fixes: After a document fails during indexing, later runs report success while silently skipping that file, leaving users unaware that the persisted index is incomplete.
• Root cause: SearchIndex.filecheck treats the nonempty sentinel value ERROR exactly like a successful stored file hash when no body hash is supplied, and process_file therefore skips the document without any diagnostic.

Closes #1355.

Regression evidence

• Before: uv run pytest tests/test_agents.py::test_filecheck_warns_about_previously_failed_documents -q exited 1

• After: uv run pytest tests/test_agents.py::test_filecheck_warns_about_previously_failed_documents -q exited 0

Verification

• uv run pytest tests/test_agents.py::test_filecheck_warns_about_previously_failed_documents tests/test_agents.py::test_getting_manifest tests/test_agents.py::test_settings_model_config tests/test_agents.py::test_tool_schema tests/test_agents.py::test_empty_index_without_index_rebuild -q
• uv run prek run --all-files
• uv run pylint src packages
• uv run refurb .
• uv build --package paper-qa

The broader index-build tests require the external model credentials documented in CONTRIBUTING.md. I attempted them locally, but they stopped in the unchanged OpenAI client setup because no key is available; I have not counted those runs as passing. The focused regression and the five credential-free agent/index tests above cover the changed decision path.

Scope

• 2 files changed, +24 / -2 lines