I need to set our company logo instead of atlassian in all email templates
You need to customize atlassian's velocity templates, Jira template files are in<JIRA-INSTALL>\WEB-INF\classes\templates\email (html, subject, text) directories.
I thought just adding a global logo would do the trick? https://answers.atlassian.com/questions/28723/how-to-set-our-company-logo-in-the-email-template.
The document is here: http://confluence.atlassian.com/display/JIRA/Customising+Email+Content.
The link is not working, and the second answer is returning to this page.
The last character of the link was a period...Try agin:
http://confluence.atlassian.com/display/JIRA/Customising+Email+Content
Sorry about that! I raised a bug so Answers stops rendering URLs incorrectly.
https://jira.atlassian.com/browse/ANSWERS-444
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