Hi,
I was toying around when I tried to add mysql-native in the dependencies.
I am using vibe.d master. It seems to me that ~master is not recognized as >= *.

How to reproduce:

xxxx@xxxx:~$ ll ~/.dub/packages/
total 32
drwxr-xr-x 6 xxxx xxxx 4096 Nov 24 07:27 ddox-0.9.15
drwxr-xr-x 4 xxxx xxxx 4096 Nov 14 00:32 libevent-master
drwxr-xr-x 4 xxxx xxxx 4096 Nov 14 00:33 libev-master
drwxr-xr-x 3 xxxx xxxx 4096 Nov 24 12:38 mysql-native-master
drwxr-xr-x 4 xxxx xxxx 4096 Nov 14 00:33 openssl-master
drwxr-xr-x 7 xxxx xxxx 4096 Nov 14 00:33 vibe-d-0.7.17
drwxr-xr-x 7 xxxx xxxx 4096 Nov 18 15:32 vibe-d-0.7.18-beta.2
drwxr-xr-x 6 xxxx xxxx 4096 Nov 24 07:08 vibe-d-master
xxxx@xxxx:~$ dub init test-conflict vibe.d
Successfully created an empty project in '/home/xxxx/test-conflict'.
xxxx@xxxx:~$ cd test-conflict/

Edit package.json set dependencies as:
"vibe-d": "~master",
"mysql-native": "~master"

xxxx@xxxx:~/test-conflict$ dub
Checking dependencies in '/home/xxxx/test-conflict'
The same package is referenced in different paths:
  vibe-d ~master: /home/xxxx/.dub/packages/vibe-d-master
  vibe-d 0.7.18-beta.2: /home/xxxx/.dub/packages/vibe-d-0.7.18-beta.2
Error: Conflicting package multi-references.

Run 'dub help' for usage information.
xxxx@xxxx:~/test-conflict$ 

More infos:

xxxx@xxxx:~/test-conflict$ uname -a && dub help | tail -n1
Linux xxxx 3.11-2-amd64 #1 SMP Debian 3.11.8-1 (2013-11-13) x86_64 GNU/Linux
DUB version v0.9.20-beta.3-6-g5857c6c
xxxx@xxxx:~/test-conflict$ cat ~/.dub/packages/mysql-native-master/package.json | grep "dependencies" -A5
	"dependencies": {
		"vibe-d": {
			"version": ">=0.7.17",
			"optional": true
		}
	},