Describe the problem

Arduino sketches may contain files under subfolders:

• data
• src

🐛 After a "Save As..." operation, any subfolders are lost and the files are all moved to the root sketch folder.

To reproduce

1. Click the following link to download the demonstration sketch:
   HasSubfolders.zip
2. Unzip the downloaded file.
3. Take note of the file structure of the sketch:

   HasSubfolders/
   ├── HasSubfolders.ino
   └── src/
       └── FromSubfolder.h
   

4. Select File > Open from the Arduino IDE menus.
5. Select the HasSubfolders.ino file from the unzipped folder.
6. Select File > Save As..." from the Arduino IDE menus.
7. Save the sketch to any convenient name and location.
8. Select Sketch > Show Sketch Folder from the Arduino IDE menus.

🐛 The subfolder structure of the sketch was lost:

HasSubfoldersAfterSaveAs/
├── FromSubfolder.h
└── HasSubfoldersAfterSaveAs.ino

Expected behavior

A "Save As" operation does not make any changes to the sketch file structure.

Arduino IDE version

94d2962

Operating system

• Windows
• Linux
• macOS

Operating system version

• Windows 11
• Ubuntu 22.04
• macOS Ventura

Additional context

I bisected the regression to 0ab2826 (the fault does not occur when using 2aad0e3).

Additional reports

• Subfolder structure of sketch lost after "Save As" operation #2077 (comment)
• https://forum.arduino.cc/t/ide-2-2-1-save-as-does-not-copy-subfolders-correctly/1191437

Issue checklist

• I searched for previous reports in the issue tracker
• I verified the problem still occurs when using the latest nightly build
• My report contains all necessary details