src/main/java/dev/frogmc/thyroxine/api/data/MappingBundle.java

@@ -69,7 +69,20 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 	}
 
 	public MappingData forNamespaces(String src, String dst) {
-		return flatten(src, dst);
+		return flattenInternal(src, dst, false);
+	}
+
+	public MappingData forNamespaces(String src, String dst, boolean allowIncomplete) {
+		return flattenInternal(src, dst, allowIncomplete);
+	}
+
+	public MappingBundle flatten(String src, String dst) {
+		return flatten(src, dst, false);
+	}
+
+	public MappingBundle flatten(String src, String dst, boolean allowIncomplete) {
+		MappingData data = flattenInternal(src, dst, allowIncomplete);
+		return new MappingBundle(data, get(data.dstNamespace()));
 	}
 
 	public DocumentationData docsForNamespace(String ns) {
@@ -78,7 +91,7 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 			if (d.namespace().equals(ns)) {
 				result.insert(d);
 			} else {
-				Mapper mappings = new Mapper(forNamespaces(d.namespace(), ns), a -> Collections.emptyList());
+				Mapper mappings = new Mapper(forNamespaces(d.namespace(), ns, false), a -> Collections.emptyList());
 				DocumentationData remapped = new DocumentationData(ns);
 				// TODO is there something we can do about the packages...? (don't think so)
 				d.classes().forEach(c -> {
@@ -98,19 +111,29 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 	}
 
 	public MappingBundle flatten() {
-		MappingData data = flattenData();
+		return flatten(false);
+	}
+
+	public MappingBundle flatten(boolean allowIncomplete) {
+		MappingData data = flattenData(allowIncomplete);
 		return new MappingBundle(data, get(data.dstNamespace()));
 	}
 
-	public MappingData flattenData() {
+	public MappingData flattenData(boolean allowIncomplete) {
+		Set<String> overlayNs = new HashSet<>();
+		for (MappingData d : data()) {
+			if (d.srcNamespace().equals(d.dstNamespace())) {
+				overlayNs.add(d.srcNamespace());
+			}
+		}
 		List<String> srcNs = srcNamespaces();
 		List<String> dstNs = dstNamespaces();
-		List<String> srcNsCandidates = srcNs.stream().filter(s -> !dstNs.contains(s)).toList();
+		List<String> srcNsCandidates = srcNs.stream().distinct().filter(s -> !dstNs.contains(s) && !overlayNs.contains(s)).toList();
-		List<String> dstNsCandidates = dstNs.stream().filter(s -> !srcNs.contains(s)).toList();
+		List<String> dstNsCandidates = dstNs.stream().distinct().filter(s -> !srcNs.contains(s) || overlayNs.contains(s)).toList();
 		if (srcNsCandidates.size() > 1) {
 			throw new IllegalStateException("Not a linear graph, cannot flatten! Got possible roots: " + String.join(", ", srcNsCandidates));
 		} else if (srcNsCandidates.isEmpty()) {
-			throw new IllegalStateException("Not a linear graph, cannot flatten! Got no possible roots! SrcNamespaces: " + String.join(", ", srcNs));
+			throw new IllegalStateException("Not a linear graph, cannot flatten! Got no possible roots! SrcNamespaces: " + String.join(", ", srcNs) + " Overlays: " + String.join(", ", overlayNs));
 		}
 		if (dstNsCandidates.size() > 1) {
 			throw new IllegalStateException("Not a linear graph, cannot flatten! Got possible ends: " + String.join(", ", dstNsCandidates));
@@ -119,10 +142,10 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 		}
 		String srcRoot = srcNsCandidates.getFirst();
 		String dstRoot = dstNsCandidates.getFirst();
-		return flatten(srcRoot, dstRoot);
+		return flattenInternal(srcRoot, dstRoot, allowIncomplete);
 	}
 
-	private MappingData flatten(String srcRoot, String dstRoot) {
+	private MappingData flattenInternal(String srcRoot, String dstRoot, boolean allowIncomplete) {
 		Deque<MappingData> path = computePath(srcRoot, dstRoot).reversed();
 
 		MappingData result = new MappingData(srcRoot, dstRoot);
@@ -140,12 +163,14 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 				String w = res;
 				res = d.classes().get(res);
 				if (res == null) {
+					if (!allowIncomplete) {
 						/*
 						 * The mapping set is incomplete at this point.
 						 * We're using the last available value to prevent incompleteness
 						 * in the resulting set.
 						 */
 						res = w;
+					}
 					break;
 				}
 			}
@@ -167,12 +192,14 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 				owner = mapper.map(owner);
 				desc = mapper.mapMethodDesc(desc);
 				if (res == null) {
+					if (!allowIncomplete) {
 						/*
 						 * The mapping set is incomplete at this point.
 						 * We're using the last available value to prevent incompleteness
 						 * in the resulting set.
 						 */
 						res = w;
+					}
 					break;
 				}
 			}
@@ -194,12 +221,14 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 				owner = mapper.map(owner);
 				desc = mapper.mapDesc(desc);
 				if (res == null) {
+					if (!allowIncomplete) {
 						/*
 						 * The mapping set is incomplete at this point.
 						 * We're using the last available value to prevent incompleteness
 						 * in the resulting set.
 						 */
 						res = w;
+					}
 					break;
 				}
 			}
@@ -234,7 +263,7 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 
 		Deque<MappingData> path = new ArrayDeque<>();
 		List<MappingData> available = new ArrayList<>(data);
-		for (MappingData d : new ArrayList<>(available)) {
+		for (MappingData d : data) {
 			if (d.srcNamespace().equals(srcRoot)) {
 				path.push(d);
 				available.remove(d);
@@ -274,6 +303,16 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 		return insert(data).insert(documentation);
 	}
 
+	public MappingBundle insert(MappingBundle other) {
+		return insert(other.data, other.documentation);
+	}
+
+	public MappingBundle insert(List<MappingData> data, List<DocumentationData> documentation) {
+		data.forEach(this::insert);
+		documentation.forEach(this::insert);
+		return this;
+	}
+
 	public DocumentationData get(String namespace) {
 		DocumentationData result = null;
 		for (DocumentationData d : documentation) {
@@ -304,4 +343,8 @@ public record MappingBundle(List<MappingData> data, List<DocumentationData> docu
 		reversed.documentation.addAll(documentation);
 		return reversed;
 	}
+
+	public MappingData flattenData() {
+		return flattenData(false);
+	}
 }

src/main/java/dev/frogmc/thyroxine/parser/tiny/TinyV2Parser.java

@@ -103,7 +103,7 @@ public class TinyV2Parser {
 				}
 
 				if (currentF == null && currentM == null) {
-					throw new IllegalStateException("Field javadoc/Method parameter mapping/javadoc specified before a declaration");
+					continue;
 				}
 
 				{

src/main/java/dev/frogmc/thyroxine/provider/ParchmentProvider.java

@@ -115,7 +115,7 @@ public class ParchmentProvider {
 							javadoc.add("@parameter " + puC.get("name") + " " + doc);
 						}
 					}
-					methods.add(new DocumentationData.Method(uc.get("name"), uc.get("descriptor"), javadoc));
+					methods.add(new DocumentationData.Method(uc.get("name"), uc.get("descriptor"), Objects.requireNonNullElse(javadoc, new ArrayList<>())));
 				});
 
 				List<UnmodifiableConfig> fieldsList = Objects.requireNonNullElse(config.get("fields"), Collections.emptyList());

src/main/java/dev/frogmc/thyroxine/writer/tiny/TinyV1Writer.java

@@ -17,7 +17,12 @@ public class TinyV1Writer {
 	 * @param writer a writer for the mappings to be written to
 	 */
 	public static void write(MappingBundle bundle, Writer writer) {
-		MappingData data = bundle.flattenData(); // we can only have 2 namespaces.
+		MappingData data;
+		if (bundle.srcNamespaces().size() > 1 || bundle.dstNamespaces().size() > 1) {
+			data = bundle.flattenData(); // we can only have 2 namespaces.
+		} else {
+			data = bundle.data().getFirst();
+		}
 
 		PrintWriter print = new PrintWriter(writer, true);
 		print.println("v1\t" + data.srcNamespace() + "\t" + data.dstNamespace());

src/main/java/dev/frogmc/thyroxine/writer/tiny/TinyV2Writer.java

@@ -14,9 +14,15 @@ public class TinyV2Writer {
 
 	public static void write(MappingBundle bundle, Writer writer) {
 
+		Set<String> overlayNs = new HashSet<>();
+		for (MappingData d : bundle.data()) {
+			if (d.srcNamespace().equals(d.dstNamespace())) {
+				overlayNs.add(d.srcNamespace());
+			}
+		}
 		List<String> srcNs = bundle.srcNamespaces();
 		List<String> dstNs = bundle.dstNamespaces();
-		List<String> srcNamespaces = srcNs.stream().filter(s -> !dstNs.contains(s)).toList();
+		List<String> srcNamespaces = srcNs.stream().distinct().filter(s -> !dstNs.contains(s) && !overlayNs.contains(s)).toList();
 		if (srcNamespaces.size() > 1) {
 			throw new IllegalStateException("Mapping Data cannot be reduced to a single source namespace, " +
 											"please use .flatten(...) to obtain a mappings set with defined namespaces");
@@ -32,27 +38,6 @@ public class TinyV2Writer {
 		List<Mapper> reverseMappers = new ArrayList<>();
 
 		String src = srcNamespace;
-		/*MappingData data = bundle.getWithSrcNamespace(src);
-		DocumentationData docs = bundle.get(src);
-		data.classes().forEach((s, s2) -> classes.computeIfAbsent(s, a -> new HashMap<>()).put(0, s2));
-		data.methods().forEach((member, s) -> methods.computeIfAbsent(member.owner(), a -> new HashMap<>())
-			.computeIfAbsent(member, a -> new HashMap<>()).put(0, s));
-		data.fields().forEach((member, s) -> fields.computeIfAbsent(member.owner(), a -> new HashMap<>())
-			.computeIfAbsent(member, a -> new HashMap<>()).put(0, s));
-		data.parameters().forEach((member, map) -> {
-			Map<Integer, Map<Integer, String>> b = parameters.computeIfAbsent(member, a -> new HashMap<>());
-			map.forEach((i, s) -> {
-				b.computeIfAbsent(i, a -> new HashMap<>()).put(0, s);
-			});
-		});
-		reverseMappers.addFirst(new Mapper(data.reverse(), s -> Collections.emptyList()));
-		if (docs != null) {
-			docs.classes().forEach(c -> {
-				if (c.javadoc() != null) {
-					javadocs.put(c.name(), String.join("\n", c.javadoc()));
-				}
-			});
-		}*/
 
 		MappingData data = bundle.getWithSrcNamespace(src);
 		DocumentationData docs;
@@ -77,7 +62,7 @@ public class TinyV2Writer {
 					DocumentationData.Class c = docsClasses.get(k);
 					if (c != null) {
 						if (c.javadoc() != null && !c.javadoc().isEmpty()) {
-							javadocs.put(root, String.join("\n", c.javadoc()));
+							javadocs.put(root, String.join("\\n", c.javadoc()));
 						}
 					}
 				}
@@ -99,7 +84,7 @@ public class TinyV2Writer {
 						c.getMethod(data.methods().get(key), selfMap.mapMethodDesc(key.descriptor()))
 							.ifPresent(m -> {
 								if (m.javadoc() != null && !m.javadoc().isEmpty()) {
-									javadocs.put(rt.owner() + rt.descriptor() + rt.name(), String.join("\n", m.javadoc()));
+									javadocs.put(rt.owner() + rt.descriptor() + rt.name(), String.join("\\n", m.javadoc()));
 								}
 							});
 					}
@@ -122,7 +107,7 @@ public class TinyV2Writer {
 						c.getField(data.fields().get(member), selfMap.mapDesc(member.descriptor()))
 							.ifPresent(f -> {
 								if (f.javadoc() != null && !f.javadoc().isEmpty()) {
-									javadocs.put(id, String.join("\n", f.javadoc()));
+									javadocs.put(id, String.join("\\n", f.javadoc()));
 								}
 							});
 					}