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/diagrams_document.md

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+# 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.