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/combined_document.md

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+# Combined LEVEL3 Feature Document {#combined}
+
+This document exercises all LEVEL3 constructs in a single file.
+
+## Introduction {#intro}
+
+This document demonstrates the full LEVEL3 feature set as described by [@smith2020].
+See [Background][bg] for context.
+
+## Background {#bg}
+
+Context and prerequisites are discussed here. Refer to [Introduction][intro]
+for the problem statement.
+
+## Architecture {#arch-section}
+
+The system architecture is shown below.
+
+![System Architecture](arch.png){#fig:arch}
+
+The architecture overview in [Architecture][arch-section] establishes the
+baseline from which the data flow is derived.
+
+## Data Flow
+
+The data flow diagram illustrates message routing.
+
+```mermaid
+graph LR
+    A[Input] --> B[Processor]
+    B --> C[Output]
+```
+
+## Algorithm {#algo}
+
+The algorithm formalises the approach described in [@jones2021].
+
+```graphviz
+digraph algorithm {
+    start -> step1 -> step2 -> end;
+}
+```
+
+## Results {#results}
+
+Experimental results confirm the algorithm in [Algorithm][algo].
+
+![Experimental Results](results.png){#fig:results}
+
+The results align with predictions from [@brown2019] and the architectural
+choices described in [Architecture][arch-section].
+
+## Conclusion {#conclusion}
+
+All LEVEL3 constructs — cross-references, figures, diagrams, and citations —
+have been demonstrated. See [Introduction][intro] through [Results][results]
+for the complete narrative.
+
+## References
+
+- [@smith2020]: Smith, J. *LEVEL3 Design Principles*. 2020.
+- [@jones2021]: Jones, B. *Algorithm Formalisation*. 2021.
+- [@brown2019]: Brown, C. *Experimental Validation*. 2019.