fix: Include dependency substitutions in dependency extractors

affected-paths/core/src/main/kotlin/com/squareup/affected/paths/core/CoreOptions.kt

@@ -95,6 +95,7 @@ public data class CoreOptions @JvmOverloads constructor(
 
   internal val gradleArgs: List<String> = buildList {
     addAll(customGradleFlags)
+    add("-PuseIncludeBuild=$useIncludeBuild")
     if (autoInjectPlugin) {
       add("-I")
       add(

affected-paths/core/src/test/kotlin/com/squareup/affected/paths/core/git/AffectedPathsTest.kt

@@ -292,7 +292,10 @@ class AffectedPathsTest {
         val result = analyzer.analyze()
 
         assertContentEquals(listOf("build2/foobar", "app", "library"), result.projectMap.keys)
-        assertContentEquals(listOf("build2/foobar"), result.affectedResults.flatMap { it.affectedProjectPaths }.distinct())
+        assertContentEquals(
+            listOf("app", "app:debug:debugUnitTest", "build2/foobar", "app:release:releaseUnitTest"),
+            result.affectedResults.flatMap { it.affectedProjectPaths }.distinct()
+        )
     }
 
     @Test

gradle.properties

@@ -29,4 +29,4 @@ SONATYPE_STAGING_PROFILE=com.squareup
 
 SONATYPE_HOST=S01
 RELEASE_SIGNING_ENABLED=true
-SONATYPE_AUTOMATIC_RELEASE=true
+SONATYPE_AUTOMATIC_RELEASE=true

tooling/support/android/src/main/kotlin/com/squareup/tooling/support/android/VariantExtractor.kt

@@ -19,8 +19,7 @@ package com.squareup.tooling.support.android
 
 import com.android.build.gradle.api.BaseVariant
 import com.squareup.tooling.models.SquareDependency
-import com.squareup.tooling.support.core.extractors.extractDependencies
-import com.squareup.tooling.support.core.extractors.extractSquareDependency
+import com.squareup.tooling.support.core.extractors.extractSquareDependencies
 import org.gradle.api.Project
 import java.io.File
 
@@ -77,8 +76,7 @@ internal fun BaseVariant.extractSquareVariantConfigurationParams(
     addAll(compileConfiguration.extendsFrom.map { it.name })
   }.toTypedArray()
 
-  val deps = project.configurations.extractDependencies(*configNames)
-    .map { it.extractSquareDependency(project) }
+  val deps = project.configurations.extractSquareDependencies(project, *configNames)
 
   return srcs to deps.toSet()
 }

tooling/support/android/src/test/kotlin/com/squareup/tooling/support/android/VariantExtractorsTest.kt

@@ -53,7 +53,11 @@ class VariantExtractorsTest {
       "All source paths must be relative to the project dir"
     )
     assertEquals(24, srcs.size, "Sources were missing")
-    assertTrue("No dependencies should be listed") { deps.isEmpty() }
+    // Filter out the kotlin-stdlib-jdk8 dependency
+    val filteredDeps = deps.filterNot {
+      it.target.contains("kotlin-stdlib")
+    }
+    assertTrue("No dependencies should be listed") { filteredDeps.isEmpty() }
   }
 
   @Test

tooling/support/core/src/main/kotlin/com/squareup/tooling/support/core/extractors/DependencyExtractors.kt

@@ -20,21 +20,77 @@ package com.squareup.tooling.support.core.extractors
 import com.squareup.tooling.models.SquareDependency
 import com.squareup.tooling.support.core.models.SquareDependency
 import org.gradle.api.Project
+import org.gradle.api.artifacts.Configuration
 import org.gradle.api.artifacts.ConfigurationContainer
 import org.gradle.api.artifacts.Dependency
 import org.gradle.api.artifacts.ProjectDependency
+import org.gradle.api.artifacts.result.ResolvedDependencyResult
+import org.gradle.api.internal.artifacts.DefaultProjectComponentIdentifier
 import org.gradle.api.internal.artifacts.dependencies.AbstractExternalModuleDependency
 import org.gradle.api.internal.artifacts.dependencies.AbstractModuleDependency
 
-// Extracts Gradle Dependency objects from the given configurations
-public fun ConfigurationContainer.extractDependencies(
+public fun ConfigurationContainer.extractSquareDependencies(
+  project: Project,
   vararg configurationNames: String
-): Sequence<Dependency> {
-  return configurationNames.asSequence().flatMap { configurationName ->
-    getByName(configurationName).allDependencies.asSequence()
-  }
+): Sequence<SquareDependency> {
+  val useIncludeBuild = project.findProperty("useIncludeBuild") == "true"
+  return configurationNames.asSequence()
+    .map { configurationName -> getByName(configurationName) }
+    .flatMap { configuration ->
+      sequence {
+        yieldAll(configuration.extractDependencies()
+          .map { it.extractSquareDependency(project) })
+        if (useIncludeBuild) {
+          yieldAll(configuration.extractResolvedProjectDependencies())
+        }
+      }
+    }
+}
+
+/**
+ * Extracts Gradle Dependency objects from the given configurations
+ */
+public fun Configuration.extractDependencies(): Sequence<Dependency> {
+  return allDependencies.asSequence()
+}
+
+/**
+ * Extracts project dependencies from the resolved artifacts of the configuration.
+ *
+ * In cases where an included build is used (e.g., through `includeBuild`), project dependencies
+ * may not appear in the standard `Configuration.allDependencies` list. Instead, they are
+ * resolved during the configuration resolution process.
+ *
+ * It only works if the configuration can be resolved (`isCanBeResolved` is true), which excludes
+ * configurations like `compileOnly`.
+ */
+public fun Configuration.extractResolvedProjectDependencies(): Sequence<SquareDependency> {
+  if (!isCanBeResolved) return emptySequence()
+
+  val resolutionResult = incoming.resolutionResult
+  val allDependencies = resolutionResult.allDependencies
+  val directDependencies = resolutionResult.root.dependencies.toSet()
+
+  return allDependencies.asSequence()
+    .mapNotNull { it as? ResolvedDependencyResult }
+    .mapNotNull { resolvedDependencyResult ->
+      val identifier = resolvedDependencyResult.selected.id as? DefaultProjectComponentIdentifier
+      identifier?.let {
+        if (it.identityPath.path != ":") {
+          val path = gradlePathToFilePath(it.identityPath.path)
+          val isTransitive = resolvedDependencyResult !in directDependencies
+          SquareDependency(
+            target = path,
+            tags = if (isTransitive) setOf("transitive") else emptySet()
+          )
+        } else {
+          null
+        }
+      }
+    }
 }
 
+
 // Converts the given Gradle Dependency into a SquareDependency use to construct the model project
 public fun Dependency.extractSquareDependency(project: Project): SquareDependency {
   return when (this) {
@@ -71,7 +127,7 @@ public fun Dependency.extractSquareDependency(project: Project): SquareDependenc
 // Meant to de-duplicate project name from target string.
 private fun Dependency.keyRelativeTo(relative: String = ""): String {
   if (this is ProjectDependency) {
-    return dependencyProject.path.replace(':', '/')
+    return gradlePathToFilePath(dependencyProject.path)
   }
   val s = group?.split(".", ":", "/") ?: emptyList()
   val result = when (s.firstOrNull()) {
@@ -80,3 +136,7 @@ private fun Dependency.keyRelativeTo(relative: String = ""): String {
   }
   return result.plus(name).joinToString("") { "/$it" }
 }
+
+private fun gradlePathToFilePath(path: String): String {
+  return path.replace(':', '/')
+}

tooling/support/core/src/test/kotlin/com/squareup/tooling/support/core/DependencyExtractorsTests.kt

@@ -18,7 +18,9 @@
 package com.squareup.tooling.support.core
 
 import com.squareup.tooling.support.core.extractors.extractDependencies
+import com.squareup.tooling.support.core.extractors.extractResolvedProjectDependencies
 import com.squareup.tooling.support.core.extractors.extractSquareDependency
+import com.squareup.tooling.support.core.models.SquareDependency
 import org.gradle.testfixtures.ProjectBuilder
 import org.junit.jupiter.api.Test
 import kotlin.test.assertEquals
@@ -34,7 +36,7 @@ class DependencyExtractorsTests {
     project.dependencies.add("testConfig", "com.squareup:foo")
     project.dependencies.add("testConfig", "com.squareup:bar")
 
-    val result = project.configurations.extractDependencies("testConfig").toList()
+    val result = project.configurations.getByName("testConfig").extractDependencies().toList()
 
     // Test
     assertEquals(2, result.size)
@@ -106,4 +108,35 @@ class DependencyExtractorsTests {
       return@assertTrue result.target == "/squareTest"
     }
   }
+
+  @Test
+  fun `test extractResolvedProjectDependencies() with empty project dependencies`() {
+    // Setup
+    val project = ProjectBuilder.builder().build()
+    project.configurations.create("testConfig")
+
+    // Test
+    val configuration = project.configurations.getByName("testConfig")
+
+    val result = configuration.extractResolvedProjectDependencies()
+    assertTrue(result.none(), "The result should be an empty sequence")
+  }
+
+  @Test
+  fun `test extractResolvedProjectDependencies() with resolved project dependencies`() {
+    // Setup
+    val project = ProjectBuilder.builder().build()
+    project.configurations.create("testConfig")
+    val projectDependency = ProjectBuilder.builder().withName("squareTest").withParent(project).build()
+    projectDependency.configurations.create("default")
+    project.dependencies.add("testConfig", projectDependency)
+
+    // Test
+    val configuration = project.configurations.getByName("testConfig")
+
+    val result = configuration.extractResolvedProjectDependencies()
+    assertEquals(1, result.count())
+    assertTrue(result.contains(SquareDependency(target = "/squareTest")))
+  }
+
 }

tooling/support/jvm/src/main/kotlin/com/squareup/tooling/support/jvm/KotlinExtractorSupport.kt

@@ -19,8 +19,7 @@ package com.squareup.tooling.support.jvm
 
 import com.squareup.tooling.models.SquareDependency
 import com.squareup.tooling.models.SquareTestConfiguration
-import com.squareup.tooling.support.core.extractors.extractDependencies
-import com.squareup.tooling.support.core.extractors.extractSquareDependency
+import com.squareup.tooling.support.core.extractors.extractSquareDependencies
 import com.squareup.tooling.support.core.models.SquareTestConfiguration
 import org.gradle.api.Project
 import org.gradle.api.tasks.SourceSet
@@ -33,10 +32,11 @@ internal fun KotlinSourceSet.extractSquareTestConfiguration(
 ): SquareTestConfiguration {
   return SquareTestConfiguration(
     srcs = kotlin.sourceDirectories.map { it.toRelativeString(project.projectDir) }.toSet(),
-    deps = project.configurations.extractDependencies(
+    deps = project.configurations.extractSquareDependencies(
+      project,
       implementationMetadataConfigurationName,
       compileOnlyMetadataConfigurationName
-    ).map { it.extractSquareDependency(project) }.toSet()
+    ).toSet()
   )
 }
 
@@ -78,8 +78,7 @@ internal fun KotlinSourceSet.extractSquareVariantConfigurationParams(
     )
   }.toTypedArray()
 
-  val result = project.configurations.extractDependencies(*configNames)
-    .map { it.extractSquareDependency(project) }.toList()
+  val result = project.configurations.extractSquareDependencies(project,*configNames).toList()
   deps.addAll(result)
 
   return srcs to deps

tooling/support/jvm/src/main/kotlin/com/squareup/tooling/support/jvm/TestVariantExtractor.kt

@@ -18,8 +18,7 @@
 package com.squareup.tooling.support.jvm
 
 import com.squareup.tooling.models.SquareTestConfiguration
-import com.squareup.tooling.support.core.extractors.extractDependencies
-import com.squareup.tooling.support.core.extractors.extractSquareDependency
+import com.squareup.tooling.support.core.extractors.extractSquareDependencies
 import com.squareup.tooling.support.core.models.SquareTestConfiguration
 import org.gradle.api.Project
 import org.gradle.api.tasks.SourceSet
@@ -28,7 +27,9 @@ import org.gradle.api.tasks.SourceSet
 internal fun SourceSet.extractSquareTestConfiguration(project: Project): SquareTestConfiguration {
   return SquareTestConfiguration(
     srcs = allSource.sourceDirectories.map { it.toRelativeString(project.projectDir) }.toSet(),
-    deps = project.configurations.extractDependencies(compileClasspathConfigurationName)
-      .map { it.extractSquareDependency(project) }.toSet()
+    deps = project.configurations.extractSquareDependencies(
+      project,
+      compileClasspathConfigurationName
+    ).toSet()
   )
 }

tooling/support/jvm/src/main/kotlin/com/squareup/tooling/support/jvm/VariantExtractor.kt

@@ -18,8 +18,7 @@
 package com.squareup.tooling.support.jvm
 
 import com.squareup.tooling.models.SquareDependency
-import com.squareup.tooling.support.core.extractors.extractDependencies
-import com.squareup.tooling.support.core.extractors.extractSquareDependency
+import com.squareup.tooling.support.core.extractors.extractSquareDependencies
 import org.gradle.api.Project
 import org.gradle.api.tasks.SourceSet
 
@@ -67,10 +66,7 @@ internal fun SourceSet.extractSquareVariantConfigurationParams(
     )
   }.toTypedArray()
 
-  deps.addAll(
-    project.configurations.extractDependencies(*configNames)
-      .map { it.extractSquareDependency(project) }
-  )
+  deps.addAll(project.configurations.extractSquareDependencies(project, *configNames))
 
   return srcs to deps
 }

tooling/support/jvm/src/test/kotlin/com/squareup/tooling/support/jvm/VariantExtractorsTest.kt

@@ -106,7 +106,11 @@ class VariantExtractorsTest {
 
     val (srcs, deps) = kotlinSourceSet.extractSquareVariantConfigurationParams(appProject, "main")
     assertTrue(srcs.containsAll(listOf("src/main/java", "src/main/kotlin")))
-    assertTrue("No dependencies should be listed") { deps.isEmpty() }
+    // Filter out the kotlin-stdlib-jdk8 dependency
+    val filteredDeps = deps.filterNot {
+      it.target.contains("kotlin-stdlib")
+    }
+    assertTrue("No dependencies should be listed") { filteredDeps.isEmpty() }
   }
 
   @Test

tooling/support/src/test/kotlin/com/squareup/tooling/support/builder/SquareProjectModelBuilderTest.kt

@@ -107,7 +107,7 @@ class SquareProjectModelBuilderTest {
             ANDROID_SRC_DIRECTORY_PATHS.map { "src/main/$it" }
       )
     }
-    assertTrue(debugVariant.deps.isEmpty())
+    assertTrue(debugVariant.deps.filterNot { it.target.contains("kotlin-stdlib") }.isEmpty())
 
     val releaseVariant = requireNotNull(result.variants["release"])
     assertTrue {
@@ -116,7 +116,7 @@ class SquareProjectModelBuilderTest {
             ANDROID_SRC_DIRECTORY_PATHS.map { "src/main/$it" }
       )
     }
-    assertTrue(releaseVariant.deps.isEmpty())
+    assertTrue(releaseVariant.deps.filterNot { it.target.contains("kotlin-stdlib") }.isEmpty())
 
     // Check test variant properties
     val debugTestVariants = debugVariant.tests
@@ -186,7 +186,7 @@ class SquareProjectModelBuilderTest {
             ANDROID_SRC_DIRECTORY_PATHS.map { "src/main/$it" }
       )
     }
-    assertTrue(debugVariant.deps.isEmpty())
+    assertTrue(debugVariant.deps.filterNot { it.target.contains("kotlin-stdlib") }.isEmpty())
 
     val releaseVariant = requireNotNull(result.variants["release"])
     assertTrue {
@@ -195,7 +195,7 @@ class SquareProjectModelBuilderTest {
             ANDROID_SRC_DIRECTORY_PATHS.map { "src/main/$it" }
       )
     }
-    assertTrue(releaseVariant.deps.isEmpty())
+    assertTrue(releaseVariant.deps.filterNot { it.target.contains("kotlin-stdlib") }.isEmpty())
 
     // Check test variant properties
     val debugTestVariants = debugVariant.tests