Hi Nate,

Thanks for the reply! To answer/clarify your points:
>.hgignore should not affect files that you have explicitly tracked (e.g. with 
>`hg add job_conf.xml`)
I have a suspicion that when I tried to add a directory using Eclipse, I might 
have added the whole repository, taking it all out of .hgignore's control.

>if the file is tracked, Mercurial will attempt to update and patch the working 
>copy if there are upstream changes.
It does seem like it isn't merging or patching, just choosing one over the 
other...

>it looks like your current tip includes neither .hgignore or job_conf.xml
I did indeed try to remove those files from being tracked in the tip. This 
caused those files to be removed from my working copy when I updated.

>Your tip is also on the stable branch - do you mean to be working in two 
>branches?
I didn't know what I was doing (still dont!) when I set up the repository - it 
seemed like if I was pulling from stable automatically, I should do all of my 
work in stable. I was further confused when Eclipse pushed to default by 
default and then I ended up mangling both.

What I'm looking for now is a way to merge the last good changeset from my 
remote server 
(bf3924e<https://bitbucket.org/cganote/iu-ncgas-galaxy/commits/bf3924ee142c9667a3cf13d83b726a46eb7d2f6c?at=stable>
 Added pull..) with my last good local repo 
(6dc34fa<https://bitbucket.org/cganote/iu-ncgas-galaxy/commits/6dc34fa8149cba1bacd119b5c08268c578e9b889?at=stable>
 Refined cli runner..). Should I just pull 6dc and replace the files I need 
from bf3 manually?

Thanks so much for the advice,

Carrie Ganote
________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Thursday, February 27, 2014 8:49 AM
To: Ganote, Carrie L
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Mercurial wants to overwrite my job_conf.xml

Hi Carrie,

.hgignore should not affect files that you have explicitly tracked (e.g. with 
`hg add job_conf.xml`) - if the file is tracked, Mercurial will attempt to 
update and patch the working copy if there are upstream changes. Also, it looks 
like your current tip includes neither .hgignore or job_conf.xml:

    https://bitbucket.org/cganote/iu-ncgas-galaxy/src/tip

Your tip is also on the stable branch - do you mean to be working in two 
branches?

--nate


On Wed, Feb 26, 2014 at 6:31 PM, Ganote, Carrie L 
<cgan...@iu.edu<mailto:cgan...@iu.edu>> wrote:
Hi Galaxy devs,

I had an issue recently where I must have messed up my .hgignore file or done 
something terrible to my repository.
I created a bitbucket and pushed my instance to it. I then pulled that onto my 
laptop and hooked it all up with Eclipse. After I was happy with my code, I 
pushed to bb and tried to pull to my instance, but the job_conf.xml file was 
overwritten. I had all of my tools set up there for the instance; on my laptop 
I had removed all that because it didn't apply. Would it have messed up if I 
deleted the file on my laptop and replaced it with a copy of 
job_conf.xml.simple? I took the .simple out of course and altered it to just 
what I needed.

This is cross-posted with Stack Overflow:
http://stackoverflow.com/questions/22055348/mercurial-update-seems-to-overwrite-local-file
Here is my repo:
https://bitbucket.org/cganote/iu-ncgas-galaxy

Any help would be greatly appreciated.

-Carrie

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