Fix resources exclusion in a multi-module project with git repo (#257)

plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java

@@ -270,7 +270,7 @@ private static StringBuilder repeat(int repeat) {
 
     public Collection<Path> listSources() {
         // Use a sorted collection so that gradle input detection isn't thrown off by ordering
-        Set<Path> result = new TreeSet<>(omniParser(emptySet()).acceptedPaths(baseDir, project.getProjectDir().toPath()));
+        Set<Path> result = new TreeSet<>(omniParser(emptySet(), project).acceptedPaths(baseDir, project.getProjectDir().toPath()));
         //noinspection deprecation
         JavaPluginConvention javaConvention = project.getConvention().findPlugin(JavaPluginConvention.class);
         if (javaConvention != null) {
@@ -809,7 +809,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
                     if (resourcesDir.exists() && !alreadyParsed.contains(resourcesDir.toPath())) {
-                        OmniParser omniParser = omniParser(alreadyParsed);
+                        OmniParser omniParser = omniParser(alreadyParsed, subproject);
                         List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
                                 sourceSetSourceFiles,
@@ -958,7 +958,7 @@ private SourceFileStream parseGradleWrapperFiles(Collection<PathMatcher> exclusi
         Stream<SourceFile> sourceFiles = Stream.empty();
         int fileCount = 0;
         if (project == project.getRootProject()) {
-            OmniParser omniParser = omniParser(alreadyParsed);
+            OmniParser omniParser = omniParser(alreadyParsed, project);
             List<Path> gradleWrapperFiles = Stream.of(
                             "gradlew", "gradlew.bat",
                             "gradle/wrapper/gradle-wrapper.jar",
@@ -978,13 +978,13 @@ private SourceFileStream parseGradleWrapperFiles(Collection<PathMatcher> exclusi
 
     protected SourceFileStream parseNonProjectResources(Project subproject, Set<Path> alreadyParsed, ExecutionContext ctx, List<Marker> projectProvenance, Stream<SourceFile> sourceFiles) {
         //Collect any additional yaml/properties/xml files that are NOT already in a source set.
-        OmniParser omniParser = omniParser(alreadyParsed);
+        OmniParser omniParser = omniParser(alreadyParsed, subproject);
         List<Path> accepted = omniParser.acceptedPaths(baseDir, subproject.getProjectDir().toPath());
         return SourceFileStream.build("", s -> {
         }).concat(omniParser.parse(accepted, baseDir, ctx), accepted.size());
     }
 
-    private OmniParser omniParser(Set<Path> alreadyParsed) {
+    private OmniParser omniParser(Set<Path> alreadyParsed, Project project) {
         return OmniParser.builder(
                         OmniParser.defaultResourceParsers(),
                         PlainTextParser.builder()

plugin/src/main/kotlin/org/openrewrite/gradle/GradleProjectSpec.kt

@@ -241,3 +241,15 @@ class GradleSourceSetSpec(
 fun gradleProject(dir: File, init: GradleProjectSpec.()->Unit): GradleProjectSpec {
     return GradleProjectSpec(dir).apply(init).build()
 }
+
+fun commitFilesToGitRepo(dir: File) {
+    exec("git init", dir)
+    exec("git config user.email [email protected]", dir)
+    exec("git config user.name TestUser", dir)
+    exec("git add .", dir)
+    exec("git commit -m \"Initial commit\"", dir)
+}
+
+private fun exec(command: String, workingDirectory: File) {
+    Runtime.getRuntime().exec(command, null, workingDirectory)
+}

plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt

@@ -26,6 +26,8 @@ import org.junit.jupiter.api.condition.DisabledIf
 import org.junit.jupiter.api.condition.DisabledOnOs
 import org.junit.jupiter.api.condition.OS
 import org.junit.jupiter.api.io.TempDir
+import org.junit.jupiter.params.ParameterizedTest
+import org.junit.jupiter.params.provider.ValueSource
 import org.openrewrite.Issue
 import java.io.File
 
@@ -259,6 +261,66 @@ class RewriteRunTest : RewritePluginTest {
         assertThat(propertiesFile.readText()).isEqualTo("bar=baz\n")
     }
 
+    @Test
+    fun `resources in subproject committed to git are correctly processed`(
+        @TempDir projectDir: File
+    ) {
+        gradleProject(projectDir) {
+            rewriteYaml("""
+                type: specs.openrewrite.org/v1beta/recipe
+                name: org.openrewrite.ChangeFooToBar
+                recipeList:
+                  - org.openrewrite.properties.ChangePropertyKey:
+                      oldPropertyKey: foo
+                      newPropertyKey: bar
+            """)
+            buildGradle("""
+                plugins {
+                    id("org.openrewrite.rewrite")
+                    id("java")
+                }
+                
+                rewrite {
+                    activeRecipe("org.openrewrite.ChangeFooToBar")
+                }
+                
+                repositories {
+                    mavenLocal()
+                    mavenCentral()
+                    maven {
+                       url = uri("https://oss.sonatype.org/content/repositories/snapshots")
+                    }
+                }
+                
+                subprojects {
+                    apply plugin: "java"
+                
+                    repositories {
+                        mavenCentral()
+                    }
+                
+                    dependencies {
+                        implementation(project(":"))
+                        implementation("junit:junit:4.12")
+                    }
+                }
+            """.trimIndent())
+            subproject("a") {
+                sourceSet("main") {
+                    propertiesFile("test.properties", "foo=baz\n")
+                }
+            }
+        }
+        commitFilesToGitRepo(projectDir)
+
+        val result = runGradle(projectDir, "rewriteRun")
+        val rewriteRunResult = result.task(":rewriteRun")!!
+        assertThat(rewriteRunResult.outcome).isEqualTo(TaskOutcome.SUCCESS)
+
+        val propertiesFile = File(projectDir, "a/src/main/resources/test.properties")
+        assertThat(propertiesFile.readText()).isEqualTo("bar=baz\n")
+    }
+
     @Suppress("ClassInitializerMayBeStatic", "StatementWithEmptyBody", "ConstantConditions")
     @Test
     fun `Checkstyle configuration is applied as a style`(
@@ -531,7 +593,7 @@ class RewriteRunTest : RewritePluginTest {
                   - org.openrewrite.gradle.UpgradeDependencyVersion:
                       groupId: com.fasterxml.jackson.core
                       artifactId: jackson-core
-                      nevVersion: 2.16.0
+                      newVersion: 2.16.0
             """)
             settingsGradle("""
                 dependencyResolutionManagement {
@@ -573,7 +635,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
                 dependencies {
-                    implementation("com.fasterxml.jackson.core:jackson-core:2.16.1")
+                    implementation("com.fasterxml.jackson.core:jackson-core:2.16.0")
                 }
                 
                 rewrite {