Themes, Stages & Skills yes - stages might slightly be adapted to match the new integration model, but the plan is to bring them back similar to how they worked before.
Release streams are replaced by out-of-the-box structuring by JIRA projects (which is needed for the deeper integration, with releases being project-specific). Instead, we've just released (with Portfolio 1.12.2) a new concept of cross-project releases so that coordinated releases across multiple JIRA projects can be managed. (this replaces the grouping across projects). For grouping within projects, we'll consider other, more generic solutions like grouping by labels or other fields longer term.
Fantastic, thank you for the detail. I look forward to it!
For other readers, the Cross-Project Releases that replace release streams can be read about here – https://confluence.atlassian.com/display/JIRAPortfolio/Portfolio+for+JIRA+1.12+Release+Notes#PortfolioforJIRA1.12ReleaseNotes-v1.12.2-February29th,2016
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