I just hit the same problem - I wanted to remove a package that I no longer 
wanted - I went to the iceberg packages tab for the project and picked remove 
from disk and then I did a synchronise and commit. At the time I did notice 
that it didn’t show a package removal change (but I assumed that as it was 
gone, maybe you don’t show that?).

Tim

> On 31 Jul 2017, at 13:30, Esteban Lorenzano <esteba...@gmail.com> wrote:
> 
> Did you commit?
> 
>> On 31 Jul 2017, at 14:06, Esteban A. Maringolo <emaring...@gmail.com> wrote:
>> 
>> That's exactly what I did. But after synchronizing the repo, the
>> package wasn't listed on Iceberg but it still was in in the repo.
>> It happened with another package in another repo as well.
>> 
>> If it happens again I'll let you know.
>> 
>> Regards!
>> 
>> Esteban A. Maringolo
>> 
>> 
>> 2017-07-31 7:03 GMT-03:00 Esteban Lorenzano <esteba...@gmail.com>:
>>> Hi,
>>> 
>>> In iceberg, you have to go to package tab and say "remove package from disk"
>>> 
>>> Esteban
>>> 
>>>> On 30 Jul 2017, at 17:01, Esteban A. Maringolo <emaring...@gmail.com> 
>>>> wrote:
>>>> 
>>>> I got into the pharo-local/iceberg/... and git rm'ed the directory,
>>>> commited and synchronized the project in Iceberg.
>>>> 
>>>> I hope it doesn't break anything since I don't know how much "magic"
>>>> does Iceberg behind the scenes other than automating the git commands
>>>> and providing a centralized UI.
>>>> 
>>>> What is the "This is all you need to read to understand Iceberg?"
>>>> document I should read? I read its wiki, but it seems there is more to
>>>> go.
>>>> 
>>>> Regards!
>>>> 
>>>> Esteban A. Maringolo
>>>> 
>>>> 
>>>> 2017-07-30 11:28 GMT-03:00 Peter Uhnak <i.uh...@gmail.com>:
>>>>> This was supposedly fixed in April 
>>>>> https://github.com/pharo-vcs/iceberg/issues/317
>>>>> 
>>>>> however I had the same issue ~two months ago, so I had to delete the 
>>>>> packages by hand.
>>>>> 
>>>>> P
>>>>> 
>>>>> 
>>>>>> On Sun, Jul 30, 2017 at 11:04:20AM -0300, Esteban A. Maringolo wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> I'm playing around with Iceberg in Pharo 6, and even when I find the
>>>>>> workflow streamlined, but since it doesn't map 1:1 with git workflow
>>>>>> from other IDEs or command line, I find myself not knowing how to do
>>>>>> certain tasks.
>>>>>> 
>>>>>> One thing that happened is that I published a few packages to one of
>>>>>> my repos in Github, then I decided to remove one of the packages from
>>>>>> the repo, then I synchronized it but in the repo there is still is the
>>>>>> package folder for the package I removed.
>>>>>> 
>>>>>> What should I do to definitely remove those files from the commit?
>>>>>> 
>>>>>> Regards!
>>>>>> 
>>>>>> Esteban A. Maringolo
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
> 


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