For a Mac, settings are under IntelliJ IDEA | Preferences. From my understanding, it is a standard UI convention on the Mac for an application's settings to be in the menu under ApplicationName | Preferences (although I am not a Mac person). I believe that is why the settings dialog was moved there; to conform to Apple standards.
As Michael mentioned, some settings were broken out to the project structure dialog a while back. I believe it was even sooner than he mentions. I think it was in version 5 or 6 that that was done. But its menu location is consistent on the Mac and Windows (AFAIK).
"From my understanding, it is a standard UI convention on the Mac for an application's settings to be in the menu under ApplicationName | Preferences (although I am not a Mac person)."
You are correct. It's a standard location and also a standard key chord (command-comma). Fire up 20 random Mac apps and you'll find preferences in the same location using the same key chord in virtually all of them. The exceptions are apps that aren't native and apps with a pedigree that predates OS/X.
It's not clear if the original posters complaint is the menu location or the functional split. If it's the menu location, then you have no leg to stand on. JetBrains is conforming to the standards of the platform. If you don't like what JetBrains has done, you are a party of one - the rest of us are quite happy to have IntelliJ follow the standards of the platform. Just like it uses command-C to copy and not control-C.
If you're unhappy with the removal of project structure from the settings (as noted this happened a very long time ago) then it's a much more grey area. It's grey specifically because IntelliJ settings are an unholy mix of application settings, plugin settings and project settings. Some settings are independent of project, some are defaults for projects, some are overriding settings and some are project-specific. Then, of course, they pulled project structure out into it's own dialog.
Honestly I wish the Preferences would be application-wide/non-project specific only. Then they could have a separate dialog for project defaults and project-specific settings. Personally, I think project structure should remain a separate dialog. The goal should be simplification and clarity, not to shove everything back into one over-arching dialog.
I would actually be ok with the change if it was consistent. The IDE Settings dialog has project settings in it and I don't understand why. IMHO, they should be in Project Structure with the rest of project settings.
Right, that's what I was saying about project settings. There seem to be three different "classes" of items in that dialog: 1. Application settings, e.g., Notifications, 2. Project default settings, and 3. Project specific settings. An example of 2 and 3 is code style/coloring. And yes, I agree with you that the top section of the dialog (Project Settings) should be moved elsewhere. The long and the short of it is that the application settings are mostly set when you first start using the tool but the project settings are used much more often.
What version had you been using? The splitting of Project Structure from Settings happened about 4 version ago. (IntelliJ 8 maybe?).
I have never been a fan of the change and keep hoping they will change it back:-)
For a Mac, settings are under IntelliJ IDEA | Preferences. From my understanding, it is a standard UI convention on the Mac for an application's settings to be in the menu under ApplicationName | Preferences (although I am not a Mac person). I believe that is why the settings dialog was moved there; to conform to Apple standards.
As Michael mentioned, some settings were broken out to the project structure dialog a while back. I believe it was even sooner than he mentions. I think it was in version 5 or 6 that that was done. But its menu location is consistent on the Mac and Windows (AFAIK).
"From my understanding, it is a standard UI convention on the Mac for an application's settings to be in the menu under ApplicationName | Preferences (although I am not a Mac person)."
You are correct. It's a standard location and also a standard key chord (command-comma). Fire up 20 random Mac apps and you'll find preferences in the same location using the same key chord in virtually all of them. The exceptions are apps that aren't native and apps with a pedigree that predates OS/X.
It's not clear if the original posters complaint is the menu location or the functional split. If it's the menu location, then you have no leg to stand on. JetBrains is conforming to the standards of the platform. If you don't like what JetBrains has done, you are a party of one - the rest of us are quite happy to have IntelliJ follow the standards of the platform. Just like it uses command-C to copy and not control-C.
If you're unhappy with the removal of project structure from the settings (as noted this happened a very long time ago) then it's a much more grey area. It's grey specifically because IntelliJ settings are an unholy mix of application settings, plugin settings and project settings. Some settings are independent of project, some are defaults for projects, some are overriding settings and some are project-specific. Then, of course, they pulled project structure out into it's own dialog.
Honestly I wish the Preferences would be application-wide/non-project specific only. Then they could have a separate dialog for project defaults and project-specific settings. Personally, I think project structure should remain a separate dialog. The goal should be simplification and clarity, not to shove everything back into one over-arching dialog.
I would actually be ok with the change if it was consistent. The IDE Settings dialog has project settings in it and I don't understand why. IMHO, they should be in Project Structure with the rest of project settings.

Right, that's what I was saying about project settings. There seem to be three different "classes" of items in that dialog: 1. Application settings, e.g., Notifications, 2. Project default settings, and 3. Project specific settings. An example of 2 and 3 is code style/coloring. And yes, I agree with you that the top section of the dialog (Project Settings) should be moved elsewhere. The long and the short of it is that the application settings are mostly set when you first start using the tool but the project settings are used much more often.