scaffold_*_project: use synchronized folder groups so add_file isn't needed for new sources

[Jason-Abbott]

Context

While building a SwiftUI macOS app on top of scaffold_macos_project, every new Swift source file required a separate mcp__xc-project__add_file call to wire it into the .pbxproj before the build would pick it up. With Xcode 16+'s PBXFileSystemSynchronizedRootGroup, files added to a folder on disk are automatically included in the build — no project file edits required.

Problem

The Xcode/Lyrico.xcodeproj/project.pbxproj produced by scaffold_macos_project uses traditional PBXGroup + PBXFileReference + PBXSourcesBuildPhase entries (objectVersion = 60). Adding a new Foo.swift to the source folder doesn't compile until add_file is called.

For an LLM agent driving the project, this means:

• Two-step file creation (Write + add_file MCP)
• Easy to forget the second step → surprising "file not found in target" errors
• Project file churn for every new source file

Proposal

Default scaffolds (both scaffold_macos_project and scaffold_ios_project) to objectVersion = 100 with PBXFileSystemSynchronizedRootGroup for the app's source folder (and a synchronized test folder if generated). Tracking issue #282 already covers parsing/maintaining objectVersion 100 projects — this is the scaffold-side counterpart so newly created projects benefit by default.

Add a use_synchronized_folders flag (default true) to opt back into the legacy layout if needed.

Acceptance criteria

• scaffold_macos_project emits a project where the app source folder is a PBXFileSystemSynchronizedRootGroup
• scaffold_ios_project does the same
• Newly created .swift files in the synchronized folder build into the target without an add_file call
• add_file still works as a no-op (or warns) when the destination is already inside a synchronized folder
• Document the new behavior in the scaffold tool descriptions

Related

• Handle Xcode 26 objectVersion 100 project format (synchronized folders) #282 "Handle Xcode 26 objectVersion 100 project format (synchronized folders)"

👾 This issue is managed by Jig. Edits made here will be overwritten.