I've added comments to each of these issues in bitbucket, and have pated them 
inline below as well.

On Jun 16, 2011, at 5:03 AM, Peter Cock wrote:

> Hi all,
> I just tried updating one of my tools on the new hg based Galaxy Tool
> Shed and ran into some issues. I guess I'm the first person to try
> this...
> First of all, there is no clear "update" action like there used to me.
> Could that be restored please?

The requested functionality is currently possible using normal mercurial 
features ( clone -> make changes to the cloned repo -> commit changes to the 
cloned repo -> push changes to the tool shed repo ).
It is also currently possible to upload a new tarball to any "upload point" 
(position) in the tool shed repository by selecting the upload point in the 
built-in repository file browser. - The hierarchy that the uploaded tarball 
contains will be added to that upload point in the tool shed repository. - Any 
files in the uploaded tarball that do not currently exist in the tool shed 
repository will be added. - Any files that exist in the hierarchy of the 
uploaded tarball that also exist in the same location of the hierarchy of the 
repository relative to the upload point will be replaced in the repository.
It is on my list to: Delete any files that do not exist in the uploaded 
tarball's hierarchy but that do existin the same position of the tool shed 
repository's hierarchy relative to the upload point. This feature will require 
clear documented communication to the user, which I've not yet had a chance to 
do, but will soon.

> I tried using the "upload files to repository" option, and picked my
> tarball. I did not pick a location since I wanted the tar ball
> unpacked at the repository root, but this isn't what happened:

Peter, I believe this is a duplicate of # 584, correct?

> Finally, it seems there is currently no delete files action, so I
> can't fix this (delete the misplaced files) via the web interface.

You can currently delete specific files by cloning the repository, making any 
changes you want (including deleting), and committing and pushing the changes 
using mercurial's command line.
I've added it to my list to provide a feature allowing a user to select a 
specific file in the repository (hopefully using the built-in file browser) and 
deleting the file in some way that doesn't require mercurial's command line, 
but in the meantime, use the above existing feature.

> Are you expecting tool authors to work primarily at the hg level?
> Regards,
> Peter

Greg Von Kuster
Galaxy Development Team

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