Sure but it REALLY clutters up the actual project.
Having a separate area for libraries that are outside the project is cleaner and avoids having to muck with the source code to support it or any potential name collisions on files.
Also, if a local libraries directory under a sketch was supported, if an advanced user wanted to use a newer/different version of the library vs the project bundled one, it is easier to just remove that particular library's directory and the sketch code could then automatically use a library installed by the library manager. No mucking with the sketch code would be required.
As an alternative, a project could be done as a library instead and specify the needed libraries as dependencies.
And then make the sketch of the project an example.
While this wouldn't actually bundle the needed libraries,
it makes the installation of the project and installing the needed library easier for the project users since the users could use the library manager to search for and install the project (library) and the IDE library manager would also install the needed libraries if they were specified as dependencies.
Updates to the project could also be handled by the library manager.
IMO, this is a fairly workable option and does provide quite a bit of flexibility with respect to the libraries used given capabilities of library dependencies.
It depends on what the primary goal is.
If it is creating a project including bundling libraries so that the project can supply a known working environment and ALL of that can be properly source controlled, there really isn't currently a way to do that with the Arduino IDE other than tossing everything (all the needed libraries) into the sketch sketch directory - which IMO, is a mess.
If the primary goal is make it easier for the users to install the project and get up and going, then making the project a library that is known to the library manager can do that and may suffice, particularly given the project library could specify the needed libraries so that the needed libraries can automatically be installed.
And in Arduino 2.x the project library could even specify the desired/supported version(s) of a needed libraries by using the version constraints capability of the depends property. So it is nearly the same as actually including the libraries and this method would provide some additional capabilities over bundling the actual libraries.
--- bill