Fix output filename collisions and non-deterministic multi-root ordering

Disambiguate output filenames when multiple root files share the same
base name (e.g. ModuleA/Root.swift and ModuleB/Root.swift now produce
ModuleA_Root+SafeDI.swift and ModuleB_Root+SafeDI.swift).

Sort extensions before joining when multiple roots share a source file,
ensuring deterministic output regardless of task-group completion order.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: dfed

Plugins/SafeDIGenerator/SafeDIGenerateDependencyTree.swift

@@ -53,8 +53,8 @@ struct SafeDIGenerateDependencyTree: BuildToolPlugin {
 			return []
 		}
 
-		let outputFiles = rootFiles.map {
-			outputDirectory.appending(path: outputFileName(for: $0))
+		let outputFiles = zip(rootFiles, outputFileNames(for: rootFiles)).map { _, name in
+			outputDirectory.appending(path: name)
 		}
 
 		let packageRoot = context.package.directoryURL

Plugins/SafeDIPrebuiltGenerator/SafeDIGenerateDependencyTree.swift

@@ -53,8 +53,8 @@ struct SafeDIGenerateDependencyTree: BuildToolPlugin {
 			return []
 		}
 
-		let outputFiles = rootFiles.map {
-			outputDirectory.appending(path: outputFileName(for: $0))
+		let outputFiles = zip(rootFiles, outputFileNames(for: rootFiles)).map { _, name in
+			outputDirectory.appending(path: name)
 		}
 
 		let packageRoot = context.package.directoryURL

Plugins/Shared.swift

@@ -133,10 +133,27 @@ func findFilesWithRoots(in swiftFiles: [URL]) -> [URL] {
 	}
 }
 
-/// Derive the output filename for a dependency tree generated from an input Swift file.
-func outputFileName(for inputURL: URL) -> String {
-	let baseName = inputURL.deletingPathExtension().lastPathComponent
-	return "\(baseName)+SafeDI.swift"
+/// Derive unique output filenames for a set of input Swift files.
+/// If two files share the same base name (e.g. `ModuleA/Root.swift` and `ModuleB/Root.swift`),
+/// parent directory components are prepended to disambiguate (e.g. `ModuleA_Root+SafeDI.swift`).
+func outputFileNames(for inputURLs: [URL]) -> [String] {
+	let baseNames = inputURLs.map { $0.deletingPathExtension().lastPathComponent }
+
+	// Count occurrences of each base name.
+	var nameCounts = [String: Int]()
+	for name in baseNames {
+		nameCounts[name, default: 0] += 1
+	}
+
+	return zip(inputURLs, baseNames).map { url, baseName in
+		if nameCounts[baseName, default: 1] > 1 {
+			// Disambiguate by prepending the parent directory name.
+			let parent = url.deletingLastPathComponent().lastPathComponent
+			return "\(parent)_\(baseName)+SafeDI.swift"
+		} else {
+			return "\(baseName)+SafeDI.swift"
+		}
+	}
 }
 
 /// Compute a path string relative to a base directory, for use in the CSV and manifest.
@@ -165,11 +182,12 @@ func writeManifest(
 	to manifestURL: URL,
 	relativeTo base: URL,
 ) throws {
+	let fileNames = outputFileNames(for: dependencyTreeInputFiles)
 	var entries = [[String: String]]()
-	for inputURL in dependencyTreeInputFiles {
+	for (inputURL, fileName) in zip(dependencyTreeInputFiles, fileNames) {
 		entries.append([
 			"inputFilePath": relativePath(for: inputURL, relativeTo: base),
-			"outputFilePath": outputDirectory.appending(path: outputFileName(for: inputURL)).path(percentEncoded: false),
+			"outputFilePath": outputDirectory.appending(path: fileName).path(percentEncoded: false),
 		])
 	}
 	let manifest = ["dependencyTreeGeneration": entries]

Sources/SafeDITool/SafeDITool.swift

@@ -24,7 +24,7 @@ import SafeDICore
 import SwiftParser
 
 @main
-struct SafeDITool: AsyncParsableCommand, Sendable {
+struct SafeDITool: AsyncParsableCommand {
 	// MARK: Arguments
 
 	@Argument(help: "A path to a CSV file containing paths of Swift files to parse.") var swiftSourcesFilePath: String?
@@ -198,7 +198,7 @@ struct SafeDITool: AsyncParsableCommand, Sendable {
 						throw ManifestError.noRootFound(inputPath: entry.inputFilePath)
 					}
 					let code: String = if let extensions = sourceFileToExtensions[entry.inputFilePath] {
-						fileHeader + extensions.joined(separator: "\n\n")
+						fileHeader + extensions.sorted().joined(separator: "\n\n")
 					} else {
 						emptyRootContent
 					}