I've just removed my packages .julia folder and redid Pkg.init() so I 
should have new .julia/METADATA. I made a minor update to the read me of 
Phylogenetics.jl's read-me, and done Pkg.tag() to make the registered 
version 0.0.1 instead of 0.0.0 on account of some welcome changes and bug 
fixes by a contributor. Now Pkg.publish() says:

*julia> **Pkg.publish()*

*ERROR: METADATA is behind origin/metadata-v2 – run `Pkg.update()` before 
publishing*

* in publish at pkg/entry.jl:306*

* in anonymous at pkg/dir.jl:25*

* in cd at file.jl:22*

* in cd at pkg/dir.jl:25*

* in publish at pkg.jl:57*

The git log:

cd .julia/METADATA
git log

n95753:METADATA wardb$ git log

commit eef97d0d9c0bacad25507b36624ad5b7652ef57a

Author: ward9250 <[email protected]>

Date:   Sat Jan 18 03:31:04 2014 +0000



    Tag Phylogenetics v0.0.1



commit bfae06320259898aa056026352905a126f63521d

Author: Dahua Lin <[email protected]>

Date:   Fri Jan 17 16:55:12 2014 -0600



    Tag StatsBase v0.3.4



commit c389e0e9e6cdf7f8004a958e04c36d10371c6df1

Author: Steven G. Johnson <[email protected]>

Date:   Fri Jan 17 15:58:16 2014 -0500



    Tag PyCall v0.4.0



commit f1aed389a89712589e3c2141c6f2988b17e9b4d9

Merge: bbb9754 8418f37

Author: Stefan Karpinski <[email protected]>

Date:   Fri Jan 17 10:00:42 2014 -0800



    Merge pull request #517 from jverzani/pull-request/8418f379

    

commit bfae06320259898aa056026352905a126f63521d

Author: Dahua Lin <[email protected]>

Date:   Fri Jan 17 16:55:12 2014 -0600



    Tag StatsBase v0.3.4



commit c389e0e9e6cdf7f8004a958e04c36d10371c6df1

Author: Steven G. Johnson <[email protected]>

Date:   Fri Jan 17 15:58:16 2014 -0500



commit eef97d0d9c0bacad25507b36624ad5b7652ef57a

Author: ward9250 <[email protected]>

Date:   Sat Jan 18 03:31:04 2014 +0000



    Tag Phylogenetics v0.0.1



commit bfae06320259898aa056026352905a126f63521d

Author: Dahua Lin <[email protected]>

Date:   Fri Jan 17 16:55:12 2014 -0600



    Tag StatsBase v0.3.4



commit c389e0e9e6cdf7f8004a958e04c36d10371c6df1

Author: Steven G. Johnson <[email protected]>

Date:   Fri Jan 17 15:58:16 2014 -0500



    Tag PyCall v0.4.0



commit f1aed389a89712589e3c2141c6f2988b17e9b4d9

Merge: bbb9754 8418f37

Author: Stefan Karpinski <[email protected]>

Date:   Fri Jan 17 10:00:42 2014 -0800



:



On Friday, January 17, 2014 10:06:12 PM UTC, Ben Ward wrote:
>
> Hi, 
>
> I've been working on an R project as part of a PhD project for a long time 
> and so have only recently returned to take a look at the Phylogenetics.jl 
> package I started to create a while ago. Reading the documentation on 
> packages I see what look to me like changes, like publishing checking out 
> branches and such all from within Julia, this is somewhat different to the 
> set up I have: I had a repository on github and on my macbook in a folder 
> on my desktop, and this was the actual repo and when I used julia and 
> tested the package this folder was ln -s into the .julia folder, and my 
> METADATA was similarly linked into .julia. I then made commits to these 
> with the github gui for osx and just pushed changes and switched branches 
> as I needed. Is this kind of arrangement still acceptable or is there a 
> better way of updating your package and working with updating METADATA now? 
> Just think maybe I need to change my setup to avoid problems.
>
> Thanks,
> Ben.  
>

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