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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