feat: WP-0003 complete — LEVEL3 advanced features + error framework

Implements full LEVEL3 feature set: cross-references (xref.py), numbered
figures (figures.py), auto-diagrams (diagrams.py), bibliography/citations
(bibliography.py), LEVEL3 capability detection (level3.py), and structured
error/warning records (errors.py). Builder, importer, and differ updated for
LEVEL3 round-trip support. REST and MCP interfaces updated with structured
warning records. 259 tests passing.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/regression/level3/xref_document.md

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+# Introduction {#intro}
+
+This document demonstrates cross-reference support for LEVEL3 processing.
+
+## Background {#bg}
+
+The background section provides context. See [Introduction][intro] for the overview.
+
+## Methodology {#method}
+
+This section describes the approach. Refer to [Background][bg] for prerequisites,
+and see [Introduction][intro] for the original problem statement.
+
+## Results {#results}
+
+Results are discussed here. The methodology in [Methodology][method] led to these findings.
+
+## Conclusion
+
+This concludes the document. All sections from [Introduction][intro] through
+[Results][results] have been covered.