[Commands] Migrate: Avoid duplicate fix-its and manifest updates when building target for both host and destination

This is a limited cherry-pick of #8888

For example if a target is a dependency of a plugin we build it for host and destination and
produce the same fix-it twice and attempt to update manifest twice because uniquing is done
on the ModuleBuildDescriptions.

The changes do the following:

- Coalesce all the diagnostic files for the same target regardless of host or destination
  build to make it possible for `SwiftFixIt` to filter duplicate fix-its;
- Unique based on module identity to prevent duplicate setting insertion.

Resolves: rdar://155569285

Author: xedin

Fixtures/SwiftMigrate/ExistentialAnyWithCommonPluginDependencyMigration/Package.swift

@@ -0,0 +1,13 @@
+// swift-tools-version:5.8
+
+import PackageDescription
+
+let package = Package(
+    name: "ExistentialAnyMigration",
+    targets: [
+        .target(name: "Library", dependencies: ["CommonLibrary"], plugins: [.plugin(name: "Plugin")]),
+        .plugin(name: "Plugin", capability: .buildTool, dependencies: ["Tool"]),
+        .executableTarget(name: "Tool", dependencies: ["CommonLibrary"]),
+        .target(name: "CommonLibrary"),
+    ]
+)

Fixtures/SwiftMigrate/ExistentialAnyWithCommonPluginDependencyMigration/Plugins/Plugin/Plugin.swift

@@ -0,0 +1,17 @@
+import PackagePlugin
+import Foundation
+
+@main struct Plugin: BuildToolPlugin {
+    func createBuildCommands(context: PluginContext, target: Target) throws -> [Command] {
+        let tool = try context.tool(named: "Tool")
+        let output = context.pluginWorkDirectory.appending(["generated.swift"])
+        return [
+            .buildCommand(
+                displayName: "Plugin",
+                executable: tool.path,
+                arguments: [output],
+                inputFiles: [],
+                outputFiles: [output])
+        ]
+    }
+}

Fixtures/SwiftMigrate/ExistentialAnyWithCommonPluginDependencyMigration/Sources/CommonLibrary/Common.swift

@@ -0,0 +1,6 @@
+public func common() {}
+
+
+protocol P {}
+
+func needsMigration(_ p: P) {}

Fixtures/SwiftMigrate/ExistentialAnyWithCommonPluginDependencyMigration/Sources/Library/Test.swift

@@ -0,0 +1,6 @@
+import CommonLibrary
+
+func bar() {
+    generatedFunction()
+    common()
+}

Fixtures/SwiftMigrate/ExistentialAnyWithCommonPluginDependencyMigration/Sources/Tool/tool.swift

@@ -0,0 +1,13 @@
+import Foundation
+import CommonLibrary
+
+@main struct Entry {
+    public static func main() async throws {
+        common()
+        let outputPath = CommandLine.arguments[1]
+        let contents = """
+        func generatedFunction() {}
+        """
+        FileManager.default.createFile(atPath: outputPath, contents: contents.data(using: .utf8))
+    }
+}

Fixtures/SwiftMigrate/ExistentialAnyWithPluginMigration/Package.swift

@@ -0,0 +1,12 @@
+// swift-tools-version:5.8
+
+import PackageDescription
+
+let package = Package(
+    name: "ExistentialAnyMigration",
+    targets: [
+        .target(name: "Library", plugins: [.plugin(name: "Plugin")]),
+        .plugin(name: "Plugin", capability: .buildTool, dependencies: ["Tool"]),
+        .executableTarget(name: "Tool"),
+    ]
+)

Fixtures/SwiftMigrate/ExistentialAnyWithPluginMigration/Plugins/Plugin/Plugin.swift

@@ -0,0 +1,17 @@
+import PackagePlugin
+import Foundation
+
+@main struct Plugin: BuildToolPlugin {
+    func createBuildCommands(context: PluginContext, target: Target) throws -> [Command] {
+        let tool = try context.tool(named: "Tool")
+        let output = context.pluginWorkDirectory.appending(["generated.swift"])
+        return [
+            .buildCommand(
+                displayName: "Plugin",
+                executable: tool.path,
+                arguments: [output],
+                inputFiles: [],
+                outputFiles: [output])
+        ]
+    }
+}

Fixtures/SwiftMigrate/ExistentialAnyWithPluginMigration/Sources/Library/Test.swift

@@ -0,0 +1,20 @@
+protocol P {
+}
+
+func test1(_: P) {
+}
+
+func test2(_: P.Protocol) {
+}
+
+func test3() {
+    let _: [P?] = []
+}
+
+func test4() {
+    var x = 42
+}
+
+func bar() {
+    generatedFunction()
+}

Fixtures/SwiftMigrate/ExistentialAnyWithPluginMigration/Sources/Tool/tool.swift

@@ -0,0 +1,12 @@
+import Foundation
+
+@main struct Entry {
+    public static func main() async throws {
+        let outputPath = CommandLine.arguments[1]
+        let contents = """
+        func generatedFunction() {}
+        func dontmodifyme(_: P) {}
+        """
+        FileManager.default.createFile(atPath: outputPath, contents: contents.data(using: .utf8))
+    }
+}

Sources/Commands/PackageCommands/Migrate.swift

@@ -113,11 +113,11 @@ extension SwiftPackageCommand {
             // Determine all of the targets we need up update.
             let buildPlan = try buildSystem.buildPlan
 
-            var modules: [any ModuleBuildDescription] = []
+            var modules = [String: [AbsolutePath]]()
             if !targets.isEmpty {
                 for buildDescription in buildPlan.buildModules
                     where targets.contains(buildDescription.module.name) {
-                    modules.append(buildDescription)
+                    modules[buildDescription.module.name, default: []].append(contentsOf: buildDescription.diagnosticFiles)
                 }
             } else {
                 let graph = try await buildSystem.getPackageGraph()
@@ -128,7 +128,7 @@ extension SwiftPackageCommand {
                     guard module.type != .plugin, !module.implicit else {
                         continue
                     }
-                    modules.append(buildDescription)
+                    modules[buildDescription.module.name, default: []].append(contentsOf: buildDescription.diagnosticFiles)
                 }
             }
 
@@ -139,10 +139,11 @@ extension SwiftPackageCommand {
 
             var summary = SwiftFixIt.Summary(numberOfFixItsApplied: 0, numberOfFilesChanged: 0)
             let fixItDuration = try ContinuousClock().measure {
-                for module in modules {
+                for (_, diagnosticFiles) in modules {
                     let fixit = try SwiftFixIt(
-                        diagnosticFiles: module.diagnosticFiles,
+                        diagnosticFiles: diagnosticFiles,
                         categories: Set(features.flatMap(\.categories)),
+                        excludedSourceDirectories: [swiftCommandState.scratchDirectory],
                         fileSystem: swiftCommandState.fileSystem
                     )
                     summary += try fixit.applyFixIts()
@@ -176,10 +177,10 @@ extension SwiftPackageCommand {
             // manifest with newly adopted feature settings.
 
             print("> Updating manifest")
-            for module in modules.map(\.module) {
-                swiftCommandState.observabilityScope.emit(debug: "Adding feature(s) to '\(module.name)'")
+            for (name, _) in modules {
+                swiftCommandState.observabilityScope.emit(debug: "Adding feature(s) to '\(name)'")
                 try self.updateManifest(
-                    for: module.name,
+                    for: name,
                     add: features,
                     using: swiftCommandState
                 )