(Duplicating the other ticket. The icon isn't horrible, but it could be improved through this.)

Current version of Bitbucket Server only use favicon. Unfortunately Apple choose <link rel="mask-icon" ...> for icon rendered inside pinned tabs.

Please add proper configuration for this into JIRA (cloud if possible and server) similar to favicon configuration.

Related info:
https://developer.apple.com/library/ios/documentation/AppleApplications/Reference/SafariWebContent/pinnedTabs/pinnedTabs.html