The current state of the IDE, as I see it, is a set of independent tools
sitting on one side and the project data ( its files) sitting on
the other side.

There is a relationship between the project and the tools.
but it is not captured in your IDE
(or weakly: by selecting a file and then you can select a tool of your choice.)

What is missing is the association of the tools with the project.
The project could be seen as a collection of tools and associated files.
The project should be defined by the type of tooling functions
and its associated files. Those tools are part of the projects structure.

Thus you create a project. Based upon the type of the project,
a basic set of tools is added to a new project structure, under each
tool are the files for that tool. Each tool has a separate customization
file for that tool within the project.

Considering a very large project there probably needs to be a tool
for connecting the pieces together (like the 'connection' tool in
the design tool.

There can be tools (views) within a tool.
So the Qt Quick Designer has a set of sub tools,
and has a list of them in the left column similar to
a photo editor. The main menu in the design tool
has all of the buttons appropriate to the designer,
like run, debug, etc.. You don't have just one main menu.
each tool has its own main menu.

The creator coordinates the location of a editor tool within its tool
and allows the tool to be undocked.

You can add or remove tools from the project. The tools are
a part of the project structure not independent of the project.

You have a list of tools that you can add to a project. Each tool
has its own editor So when you click on that section or part
of the project its editor takes control.

The type of project determines the minimum set of tools.
They can not be deleted because that type of project requires them.
They are part of the project structure.

Some of the main menu elements become a part of the project.

The main menu "edit" function becomes a part of the tool.

The project itself has a management tool

The QtCreator then becomes a tool to manage a collection
of projects and tools.

The project manager tool is used to control the structure of
the project (sessions, etc..)

When I open a project i begin with the project manager tool.
It displays the structure of the project by tools, and the files
are listed under the tool.

Rather then keep all files in a single folder, allow the
tool to create sub folders under the project folder in which its files are stored.

I assume there will be a tool for platforms, debug, analyze, source control.
etc. All of them are listed under the project's structure as necessary rather
then in the main menu.

The creator maintains a list of tools (extensions), and projects.

The project tool can have sub tools like source control, and publishing
under its entry in the project structure.

Just a thought.