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Confluence pages can be linked to Jira issues. For examples requirements to Epics. You can create Jira reports within Confluence.
Jira issue can be linked to code using branch and commit messages. You can create branch from Jira issue and see the current status like pull request created/merged on the issues. Jira issue worklog, comments and transition can also be made using smart commits.
I don't use Sourcetree but it is a good visual/GUI based tool to look at your code.
There are plenty of examples on Atlassian website if you want to explore these features.