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