Mark removed source file as deleted for compiler

#KT-55905 Fixed

compiler/incremental-compilation-impl/src/org/jetbrains/kotlin/incremental/IncrementalCompilerRunner.kt

@@ -469,7 +469,7 @@ abstract class IncrementalCompilerRunner<
             val lookupTracker = LookupTrackerImpl(LookupTracker.DO_NOTHING)
             val expectActualTracker = ExpectActualTrackerImpl()
             //TODO(valtman) sourceToCompile calculate based on abiSnapshot
-            val (sourcesToCompile, removedKotlinSources) = dirtySources.partition(File::exists)
+            val (sourcesToCompile, removedKotlinSources) = dirtySources.partition { it.exists() && allKotlinSources.contains(it) }
 
             val services = makeServices(
                 args, lookupTracker, expectActualTracker, caches,

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/IncrementalCompilationMultiProjectIT.kt

@@ -6,6 +6,7 @@ import org.jetbrains.kotlin.build.report.metrics.BuildAttribute
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompilerExecutionStrategy
 import org.jetbrains.kotlin.gradle.testbase.*
 import org.jetbrains.kotlin.gradle.util.checkedReplace
+import org.jetbrains.kotlin.gradle.util.replaceText
 import org.junit.jupiter.api.Disabled
 import org.junit.jupiter.api.DisplayName
 import java.nio.file.Path
@@ -200,6 +201,24 @@ open class IncrementalCompilationJvmMultiProjectIT : BaseIncrementalCompilationM
         }
     }
 
+    //KT-55905
+    @DisplayName("Imncremental compilation with source set update")
+    @GradleTest
+    open fun testSourceSetAdjustment(gradleVersion: GradleVersion) {
+        val setUpExternalSource = "sourceSets[\"main\"].kotlin.srcDir(\"../external/src\")"
+        defaultProject(gradleVersion) {
+            subProject("lib").buildGradle.appendText("\n$setUpExternalSource")
+            subProject("lib")
+                .projectPath
+                .resolve("src/main/kotlin/bar/A.kt").modify {
+                    it.replace("fun a() {}","fun a() {}\nfun c() = ExternalClass()" )
+                }
+            build("assemble")
+            subProject("lib").buildGradle.replaceText(setUpExternalSource, "")
+            buildAndFail("assemble")
+        }
+    }
+
     protected fun testCompileLibWithGroovy_doTest(
         gradleVersion: GradleVersion,
         assertResults: (TestProject, BuildResult) -> Unit

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/incrementalMultiproject/external/src/external.kt

@@ -0,0 +1,5 @@
+package bar
+
+open class ExternalClass {
+    fun some() {}
+}