fix: isolate citation registries per pipeline

[ump45nose]

Summary

• isolate citation state behind a unique registry ID for each LightResearch pipeline run
• pass that ID through the generated tool metadata and release the registry when the pipeline completes
• add a focused regression test that interleaves two runs and verifies their citation counters remain independent

Root cause

init_citation_registry() reset a class-level dictionary shared by every request. Starting a second pipeline therefore erased the first pipeline's in-progress citation mappings.

Validation

• pytest -p no:cacheprovider tests/test_citation_registry.py -q
• ultrarag build examples/demos/LightResearch.yaml
• generated MCP metadata smoke for init, assign, and clear tool contracts
• ruff check --select I,F,E9 tests/test_citation_registry.py
• ruff check --select I servers/custom/src/custom.py

Fixes #394

[ump45nose]

@xhd0728 This focused LightResearch concurrency fix is ready for review. It scopes citation registries by pipeline-run ID, carries that ID through generated tool metadata, and releases the registry on completion; the regression interleaves two runs and verifies independent counters. The focused pytest, pipeline build, MCP metadata smoke, and targeted Ruff checks pass. Since you maintain and review servers/custom/src/custom.py and the related demo pipelines, could you take a look when convenient?

[xhd0728]

Thanks for the fix! The registry isolation works in our interleaved-request tests, but further testing found two issues:

1. The final answer is lost from the pipeline return value. Adding clear_citation_registry as the last step makes PipelineCall.final_result return None, even though the answer was generated successfully.
2. Cleanup is skipped on failure. If generation or retrieval raises before the last step, the registry remains in memory. Repeated failures in a reused server can accumulate these entries.

Could you move cleanup into a guaranteed lifecycle/finally path that preserves the generated result and handles failures and cancellation? Please also add regression tests for these cases before merging.