We haven't add any permission checking on the files tab, true. If we add a permission settings for files (who can see files and who can't), will that be helpful to you? In this case, we don't have any ETA, but we would love to fix that
I have the same problem. Media Files attached to a project should only be visible and searchable for project members, not every registered user on my site. Now everyone can go to the WordPress Media Dashboard and look into any file that is added to any project, even if he's not involved.
Those files should be excluded from search engines indexing too.
Actually we are renovating the WP Project Manager plugin. We are trying our best to add some major features to the plugin and planning to release a major update in the New Years eve. Currently we are working with request optimizing and privacy.
So the plugin would require lesser resource and let you keep your files with privacy. As you can see this is a huge task to do, we can not specify and ETA; but I can assure you that our team is working on it with full force.
Stay in touch by subscribing our mailing list, Twitter and Facebook page. We will let you know there about our progress.