Hrm, after some more testing it seems compilation fails when using both vibe.d and gfm.

package.json:

{
    "name": "project",
    "dependencies": {
		"vibe-d": { "version": "~master", },
		"gfm": { "version": "~master", },
    },	
}

An empty app.d:

module app;

This fails with a linker error

C:\Test
Checking dependencies in 'C:\Test'
Package gfm (configuration "library") defines no import paths, use {"importPaths": [...]} or the default package directory structure to fix this.
Copying files...
Building configuration "application", build type debug
Compiling...
Warning: -version=VibeDefaultMain will be required in the future to use vibe.d's default main(). Please update your build scripts.
Linking...
OPTLINK (R) for Win32  Release 8.00.13
Copyright (C) Digital Mars 1989-2010  All rights reserved.
http://www.digitalmars.com/ctg/optlink.html
.dub\build\application-debug-x86-dmd-DA39A3EE5E6B4B0D3255BFEF95601890AFD80709\project.obj(project)
 Error 45: Too Much DEBUG Data for Old CodeView format
--- errorlevel 1
Error executing command run: Link command failed with exit code 1