According to the announcement for JIRA 6.1, customized projects key will be supported using letters, numbers and underscores: https://confluence.atlassian.com/display/JIRA/End+of+Support+Announcements+for+JIRA#EndofSupportAnnouncementsforJIRA-20130513projectkey
According to https://confluence.atlassian.com/display/JIRACOM/Configuring+Project+Keys Greenhopper and Bamboo might not support projects with customized key pattern.
Is this note related only to JIRA < 6.1?
Will the customized project keys, following the new restrictions (introduced in 6.1), be fully supported within the other Atlassian products some time in the future?
Actually, the note "Greenhopper and Bamboo might not support projects with customized key pattern" is not related to JIRA annoucement "customized projects key will be supported using letters, numbers and underscores".
JIRA 6.1 support customized projects key with letters, numbers and underscores but GreenHopper and Bamboo might not support it.
However, the latest GreenHopper have been tested to work with customized projects key (source). You might want to check if you get any error working with customized projects key and raise it to https://support.atlassian.com
Bamboo does not support customized projects key yet. Feature request: https://jira.atlassian.com/browse/BAM-1569
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