Prevent cross-scope source files from being parsed as PlainText

When processMainSources or processTestSources runs independently
(e.g. scoped listSourceFiles), resource parsing can walk the entire
project tree if a resource directory points at the project root.
Source files belonging to the other scope are not yet in alreadyParsed,
so they get claimed by PlainTextParser. The real parse in the other
scope then produces a duplicate entry, and the PlainText version
shadows the properly typed one — making annotations invisible to
recipes like FindAnnotations.

Fix: pre-populate alreadyParsed with the opposite scope's source file
paths before resource parsing begins. This mirrors what the non-scoped
listSourceFiles gets for free by processing both scopes with a shared
alreadyParsed set.

Author: pstreef

src/main/java/org/openrewrite/maven/MavenMojoProjectParser.java

@@ -395,6 +395,9 @@ private Stream<SourceFile> processMainSources(
         List<Path> mainKotlinSources = (kotlinSourceDir != null) ? listKotlinSources(mavenProject.getBasedir().toPath().resolve(kotlinSourceDir)) : Collections.emptyList();
         alreadyParsed.addAll(mainKotlinSources);
 
+        // Prevent resource parsers from claiming test sources as PlainText
+        // when a resource directory encompasses the project root
+        collectSourceFilePaths(mavenProject.getTestCompileSourceRoots(), alreadyParsed);
         logInfo(mavenProject, "Parsing source files");
         List<Path> dependencies = mavenProject.getCompileClasspathElements().stream()
                 .distinct()
@@ -461,6 +464,10 @@ private Stream<SourceFile> processTestSources(
         List<Path> testKotlinSources = (kotlinSourceDir != null) ? listKotlinSources(mavenProject.getBasedir().toPath().resolve(kotlinSourceDir)) : Collections.emptyList();
         alreadyParsed.addAll(testKotlinSources);
 
+        // Prevent resource parsers from claiming main sources as PlainText
+        // when a resource directory encompasses the project root
+        collectSourceFilePaths(mavenProject.getCompileSourceRoots(), alreadyParsed);
+
         Stream<SourceFile> parsedJava = Stream.empty();
         if (!testJavaSources.isEmpty()) {
             parsedJava = javaParserBuilder.build().parse(testJavaSources, baseDir, ctx);
@@ -748,6 +755,21 @@ private <T extends SourceFile> UnaryOperator<T> addProvenance(Path baseDir, List
         };
     }
 
+    /**
+     * Walk the given source roots and add all Java and Kotlin file paths to the provided set.
+     * This prevents resource parsers from claiming source files belonging to another scope
+     * as PlainText when a resource directory encompasses the entire project root.
+     */
+    static void collectSourceFilePaths(List<String> sourceRoots, Set<Path> paths) throws MojoExecutionException {
+        for (String root : sourceRoots) {
+            Path rootPath = Paths.get(root);
+            if (Files.isDirectory(rootPath)) {
+                paths.addAll(listJavaSources(rootPath));
+                paths.addAll(listKotlinSources(rootPath));
+            }
+        }
+    }
+
     private static List<Path> listJavaSources(Path sourceDirectory) throws MojoExecutionException {
         return listSources(sourceDirectory, ".java");
     }