ArmDot can embed files into protected assembly. Switch to Files in the ArmDot UI:
Here the predefined folders at the right, like Assembly Directory and System Drive.
To include a file to a protected assembly click to Add Files... and choose a file. Another option is to import an entire directory.
Possible file / directory type is Embedded or External. To change it, select a file and change type via Properties at the right from the file tree.
If a directory is not marked as embedded, the protected assembly will view both real files and embedded files from the directory.