docs: polish reductions.typ with theorem labels and cleanup

.gitignore

@@ -71,3 +71,6 @@ tarpaulin-report.html
 
 # Reference packages (downloaded for comparison)
 pkgref/
+
+# Generated example outputs
+docs/paper/examples/

Makefile

@@ -1,6 +1,6 @@
 # Makefile for problemreductions
 
-.PHONY: help build test fmt clippy doc mdbook paper clean coverage rust-export compare qubo-testdata
+.PHONY: help build test fmt clippy doc mdbook paper examples clean coverage rust-export compare qubo-testdata
 
 # Default target
 help:
@@ -18,6 +18,7 @@ help:
 	@echo "  check        - Quick check (fmt + clippy + test)"
 	@echo "  rust-export  - Generate Rust mapping JSON exports"
 	@echo "  compare      - Generate and compare Rust mapping exports"
+	@echo "  examples     - Generate example JSON for paper"
 	@echo "  qubo-testdata - Regenerate QUBO test data (requires uv)"
 
 # Build the project
@@ -48,8 +49,18 @@ doc:
 mdbook:
 	mdbook serve docs --open
 
-# Build Typst paper
-paper:
+# Generate all example JSON files for the paper
+REDUCTION_EXAMPLES := $(patsubst examples/%.rs,%,$(wildcard examples/reduction_*.rs))
+examples:
+	@mkdir -p docs/paper/examples
+	@for example in $(REDUCTION_EXAMPLES); do \
+		echo "Running $$example..."; \
+		cargo run --all-features --example $$example || exit 1; \
+	done
+	cargo run --all-features --example export_petersen_mapping
+
+# Build Typst paper (generates examples first)
+paper: examples
 	cargo run --example export_graph
 	cd docs/paper && typst compile reductions.typ reductions.pdf
 

docs/paper/reduction_graph.json

@@ -418,37 +418,37 @@
     },
     {
       "source": {
-        "name": "Satisfiability",
+        "name": "MaxCut",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
         }
       },
       "target": {
-        "name": "DominatingSet",
+        "name": "SpinGlass",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
         }
       },
-      "bidirectional": false
+      "bidirectional": true
     },
     {
       "source": {
-        "name": "Satisfiability",
+        "name": "QUBO",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "Unweighted"
+          "weight": "f64"
         }
       },
       "target": {
-        "name": "IndependentSet",
+        "name": "SpinGlass",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "Unweighted"
+          "weight": "f64"
         }
       },
-      "bidirectional": false
+      "bidirectional": true
     },
     {
       "source": {
@@ -459,10 +459,10 @@
         }
       },
       "target": {
-        "name": "KColoring",
+        "name": "DominatingSet",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "i32"
+          "weight": "Unweighted"
         }
       },
       "bidirectional": false
@@ -476,58 +476,58 @@
         }
       },
       "target": {
-        "name": "KSatisfiability",
+        "name": "IndependentSet",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
         }
       },
-      "bidirectional": true
+      "bidirectional": false
     },
     {
       "source": {
-        "name": "SetPacking",
+        "name": "Satisfiability",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
         }
       },
       "target": {
-        "name": "IndependentSet",
+        "name": "KColoring",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "Unweighted"
+          "weight": "i32"
         }
       },
-      "bidirectional": true
+      "bidirectional": false
     },
     {
       "source": {
-        "name": "SetPacking",
+        "name": "Satisfiability",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "i32"
+          "weight": "Unweighted"
         }
       },
       "target": {
-        "name": "QUBO",
+        "name": "KSatisfiability",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "f64"
+          "weight": "Unweighted"
         }
       },
-      "bidirectional": false
+      "bidirectional": true
     },
     {
       "source": {
-        "name": "SpinGlass",
+        "name": "SetPacking",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
         }
       },
       "target": {
-        "name": "MaxCut",
+        "name": "IndependentSet",
         "variant": {
           "graph": "SimpleGraph",
           "weight": "Unweighted"
@@ -537,10 +537,10 @@
     },
     {
       "source": {
-        "name": "SpinGlass",
+        "name": "SetPacking",
         "variant": {
           "graph": "SimpleGraph",
-          "weight": "f64"
+          "weight": "i32"
         }
       },
       "target": {
@@ -550,7 +550,7 @@
           "weight": "f64"
         }
       },
-      "bidirectional": true
+      "bidirectional": false
     },
     {
       "source": {