I recently had an app that had been installed a while ago. In the mean time we had created a new profile type which, since it hadn't existed when the app was first installed, didn't have permissions to the app. I couldn't figure out how to update the profile's permissions so it could access the app. I ended up having to wait until an update came out so I could set the permissions again. I'm sure this is controlled somewhere but I couldn't find it anywhere. How obvious was the link I needed to do this?
Using the Enhanced Profile User Interface ( My Name -> Setup -> App Setup -> Customize -> User Interface), the Profile manager makes it very simple.
Under Manage Users -> Profiles, select the profile you want to edit. There is a screen for Assigned Apps, which will govern what the profile sees in the drop-down in the upper-right of the screen.
Governs general permissions for an app, such as Convert Leads inside Sales.
Lets you set specific permissions on fields as well as if the profile can Read, Edit, Delete the object at all.
Bulk Permissions for Apps
If you want change permissions to an application in bulk, go to My Name -> Setup -> App Setup -> Create -> Apps. Find the app, click edit, and then scroll down. You will see a list of Profiles and checkboxes that dictate if they can see the app and if it is the profile's default app.
Note: Just because a user has access to the App does not necessarily mean they have access to the Tabs inside of the App. That will be governed by their profile's Object Settings (see above.)
you can always manually enable your profile permissions; however, mapping profiles in your org to the publisher's profile settings is a singular type event during installation/upgrade. One way to copy the configurations from one profile to another is to use the Force.com IDE to compare a profile that you mapped during installation/upgrade to one that was created post installation/upgrade. Also, when you clone a profile, it will automatically carry any permissions that you may have mapped during that installation and upgrade process.