[Incremental] Fix clean build quadratic performance bug

Sources/SwiftDriver/IncrementalCompilation/DependencyKey.swift

@@ -348,15 +348,15 @@ extension DependencyKey.Designator: Comparable {}
 // MARK: - InvalidationReason
 extension ExternalDependency {
   /// When explaining incremental decisions, it helps to know why a particular external dependency
-  /// was investigated.
+  /// caused invalidation.
   public enum InvalidationReason: String, CustomStringConvertible {
     /// An `import` of this file was added to the source code.
     case added
 
     /// The imported file has changed.
     case changed
 
-    /// Used when testing invalidation
+    /// Used when testing
     case testing
 
     public var description: String { rawValue }

Sources/SwiftDriver/IncrementalCompilation/FirstWaveComputer.swift

@@ -131,13 +131,13 @@ extension IncrementalCompilationState.FirstWaveComputer {
       }
     }
 
-    let inputsHavingMalformedDependencySources =
-      sourceFiles.currentInOrder.filter { sourceFile in
-        !moduleDependencyGraph.containsNodes(forSourceFile: sourceFile)
-      }
+    let inputsMissingFromGraph = sourceFiles.currentInOrder.filter { sourceFile in
+      !moduleDependencyGraph.containsNodes(forSourceFile: sourceFile)
+    }
 
-    if let reporter = reporter {
-      for input in inputsHavingMalformedDependencySources {
+    if let reporter = reporter,
+       moduleDependencyGraph.phase == .buildingFromSwiftDeps {
+      for input in inputsMissingFromGraph {
         reporter.report("Has malformed dependency source; will queue", input)
       }
     }
@@ -156,7 +156,7 @@ extension IncrementalCompilationState.FirstWaveComputer {
     let definitelyRequiredInputs =
       Set(changedInputs.map({ $0.filePath }) +
             inputsInvalidatedByExternals +
-            inputsHavingMalformedDependencySources +
+            inputsMissingFromGraph +
             inputsMissingOutputs)
     if let reporter = reporter {
       for scheduledInput in sortByCommandLineOrder(definitelyRequiredInputs) {

Sources/SwiftDriver/IncrementalCompilation/IncrementalDependencyAndInputSetup.swift

@@ -206,7 +206,7 @@ extension IncrementalCompilationState.IncrementalDependencyAndInputSetup {
       return readPriorGraphAndCollectInputsInvalidatedByChangedOrAddedExternals()
     }
     // Every external is added, but don't want to compile an unchanged input that has an import
-    // so just changed, not changedOrAdded
+    // so just changed, not changedOrAdded.
     return buildInitialGraphFromSwiftDepsAndCollectInputsInvalidatedByChangedExternals()
   }
 
@@ -230,7 +230,13 @@ extension IncrementalCompilationState.IncrementalDependencyAndInputSetup {
     }
     guard let graph = graphIfPresent
     else {
-      return buildInitialGraphFromSwiftDepsAndCollectInputsInvalidatedByChangedExternals()
+      // Do not fall back to `buildInitialGraphFromSwiftDepsAndCollectInputsInvalidatedByChangedExternals`
+      // because it would be unsound to read a `swiftmodule` file with only a partial set of integrated `swiftdeps`.
+      // A fingerprint change in such a `swiftmodule` would not be able to propagate and invalidate a use
+      // in a as-yet-unread swiftdeps file.
+      //
+      // Instead, just compile everything. It's OK to be unsound then because every file will be compiled anyway.
+      return bulidEmptyGraphAndCompileEverything()
     }
     graph.dotFileWriter?.write(graph)
 
@@ -257,10 +263,7 @@ extension IncrementalCompilationState.IncrementalDependencyAndInputSetup {
   private func buildInitialGraphFromSwiftDepsAndCollectInputsInvalidatedByChangedExternals()
   -> (ModuleDependencyGraph, TransitivelyInvalidatedInputSet)?
   {
-    guard let graph = ModuleDependencyGraph(self, .buildingWithoutAPrior)
-    else {
-      return nil
-    }
+    let graph = ModuleDependencyGraph(self, .buildingFromSwiftDeps)
     var inputsInvalidatedByChangedExternals = TransitivelyInvalidatedInputSet()
     for input in sourceFiles.currentInOrder {
        guard let invalidatedInputs =
@@ -273,4 +276,10 @@ extension IncrementalCompilationState.IncrementalDependencyAndInputSetup {
     reporter?.report("Created dependency graph from swiftdeps files")
     return (graph, inputsInvalidatedByChangedExternals)
   }
+
+  private func bulidEmptyGraphAndCompileEverything()
+  -> (ModuleDependencyGraph, TransitivelyInvalidatedInputSet) {
+    let graph = ModuleDependencyGraph(self, .buildingAfterEachCompilation)
+    return (graph, TransitivelyInvalidatedInputSet())
+  }
 }