How can I check-in revision of an entire project ?

Revision history in WireframePro is page level. For each page, revisions are auto-created or checked-in based on the changes made. Which is explained in detail here - https://support.mockflow.com/article/59-revision-history-for-projects

However to create revision for an entire project, the whole project can be duplicated and stored as check-points -

https://support.mockflow.com/article/61-how-to-duplicate-save-as-a-project