Can you configure GitHub with custom URL?

We have a custom URL from GitHub like git1.pscpl.com. There does not seem to be any option to do that in Bamboo 5.8.1!

I am currently configuring our repositories as linked Git repositories and also specifying the repository ssh URL with the private key and branch.

It looks like I have to create a linked repository whenever I need to provide a different branch! In that sense, the bamboo linked repository is more like a 'repository + branch + key'. Is there an alternative where I can specify branch while specifying the source code checkout task or similar?

I have the same key for all my repositories. Do I need to specifically upload it whenever I specify a Bamboo linked repository? Is there a way I can just upload the key once as a global fall-back key for all repositories?

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You should be able to configure GitHub's base URL using system property atlassian.bamboo.github.api.base.url by default it is set to https://api.github.com/

Regarding your second question. Can you please describe your scenario with more details? Why is your top level Plan using branch of the repository? Did you have a chance to read this documentation: https://confluence.atlassian.com/display/BAMBOO/Using+plan+branches ?

Is there any other way to set system variable other than https://confluence.atlassian.com/display/BAMBOO/Configuring+Bamboo+on+start-up ? I am interested in knowing if there is a GUI/Web UI way to do it. (Of course, it will need restart?)

There's no GUI for that

I, too, have a github Enterprise.  The property you mention is set where?  setenv.sh?  bamboo.cfg.xml?  

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