It's rare for the Arduino developers to read the forum, even though you'd think someone would monitor this section. However, this is a good place to get some community input on a proposal. Sometimes we can resolve things here on the forum (such as when there is a solution already in place or one in the works). Other times the discussion here can refine the proposal before it is finally submitted to the developers. So the system is not completely broken.
The tool used for handling libraries is arduino-builder:
However, if this is simply a matter of changing the specification, rather than actually changing code, then that would not be the best place to submit the issue report. Instead I would recommend the arduino/Arduino repository:
In addition to containing the code for the Arduino IDE, that repository acts as the general catch-all for issue reports that aren't specific to any of the other repositories.
I recommend including the proposed text you would like to have added/removed from the specification. The specification is actually a publicly editable wiki but I don't think it would be appropriate to simply make the change on your own initiative. However, if you can get approval from a member of the Arduino team you can then go and make the edit yourself so there will be no need to wait for them to do it. I would actually state that you're willing to do this as it may make the developers more receptive to just saying "sounds good, go ahead" instead of waiting until they actually have the time.
I should clarify what I meant by "white list". The relevant part of the specification is here:
The source code found in src folder and all its subfolders is compiled and linked in the user’s sketch. Only the src folder is added to the include search path (both when compiling the sketch and the library).
...
For backward compatibility with Arduino 1.0.x, the library author may opt to place source code into the root folder, instead of the folder called src. In this case the 1.0 library format is applied and the source code is searched from the library root folder and the utility folder
So to me this is a "white list" of the library root folder, and the utility folder or the src folder for library source files. In addition there is a "black list" of sorts:
The content of the extras folder is totally ignored by the IDE
So you could maybe consider any other folders to be in a gray area. Unfortunately the Arduino IDE does not actually follow the specification regarding the extras folder since sketches in that location are still shown in the File > Examples menu. However, at least with the specification in place we can definitively consider that to be a bug and hope for it to be fixed eventually. I don't think that issue is relevant to arduino_ci since you use .cpp files rather than .ino.