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/bibliography_document.md

@@ -0,0 +1,35 @@
+# Research Document with Citations
+
+## Introduction
+
+Prior work by [@smith2020] established the foundation. The approach was later
+refined by [@jones2021], building on the original insights of [@smith2020].
+
+## Related Work
+
+Several key contributions inform this work. The landmark paper [@brown2019]
+introduced the core technique. Further development appeared in [@davis2022]
+and [@wilson2023].
+
+## Methodology
+
+Based on [@smith2020] and the refinements of [@jones2021], our methodology
+proceeds as follows.
+
+## Results
+
+Our results confirm the predictions of [@brown2019] and extend the findings
+of [@davis2022].
+
+## Conclusion
+
+This work synthesises [@smith2020], [@jones2021], [@brown2019], [@davis2022],
+and [@wilson2023].
+
+## References
+
+- [@smith2020]: Smith, J. *Foundational Work*. Journal of Research, 2020.
+- [@jones2021]: Jones, B. *Refinements and Extensions*. Proceedings, 2021.
+- [@brown2019]: Brown, C. *The Core Technique*. Nature, 2019.
+- [@davis2022]: Davis, A. *Further Development*. Science, 2022.
+- [@wilson2023]: Wilson, E. *Recent Advances*. Review, 2023.

tests/regression/level3/combined_document.md

@@ -0,0 +1,63 @@
+# 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.

tests/regression/level3/diagrams_document.md

@@ -0,0 +1,44 @@
+# Document with Diagram Sources
+
+## State Machine
+
+The following Mermaid diagram describes the state machine:
+
+```mermaid
+stateDiagram-v2
+    [*] --> Idle
+    Idle --> Processing: start
+    Processing --> Done: complete
+    Processing --> Error: fail
+    Done --> [*]
+    Error --> Idle: reset
+```
+
+## Dependency Graph
+
+The Graphviz diagram shows dependencies:
+
+```graphviz
+digraph G {
+    A -> B;
+    A -> C;
+    B -> D;
+    C -> D;
+}
+```
+
+## Sequence
+
+The PlantUML sequence diagram:
+
+```plantuml
+@startuml
+Alice -> Bob: Request
+Bob --> Alice: Response
+Alice -> Carol: Forward
+@enduml
+```
+
+## Summary
+
+All three diagram types are supported in LEVEL3 source-only mode.

tests/regression/level3/figures_document.md

@@ -0,0 +1,29 @@
+# Technical Report with Figures
+
+## Overview
+
+This document contains multiple numbered figures for LEVEL3 round-trip testing.
+
+## System Architecture
+
+The overall architecture is illustrated below.
+
+![System Architecture Overview](figures/architecture.png){#fig:arch}
+
+The architecture shows the main components and their interactions.
+
+## Data Flow
+
+The data flow is shown in the following figure.
+
+![Data Flow Diagram](figures/dataflow.png){#fig:dataflow}
+
+Compare the architecture in [fig:arch] with the data flow above.
+
+## Results
+
+Final results are captured in this chart.
+
+![Results Summary Chart](figures/results.png){#fig:results}
+
+The chart confirms the findings from the data flow in Figure 2.

tests/regression/level3/xref_document.md

@@ -0,0 +1,21 @@
+# 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.