A bit more background.
When the new library format was introduced at IDE 1.5 the arduino team was proposing some mechanisms to separate out the libraries for different cores.
You can read this for some information but it doesn't have some information about the early iterations:
At the time, the arduino team clearly did not understand some of complexities of supporting multiple cores and the issues for 3rd party developers, which are very different from the IDE bundled libraries and cores.
Believe it or not the first 1.5x format did not support backward compatibility with all the existing 1.x libraries.
This was essentially a repeat of the disaster of the decision that the Arduino team made when going from 1.0 RC to the official 1.0 release where 100% of all the existing 3rd party code would break.
Against some of the core Arduino team, I managed to talk the main Arduino developer into providing backward compatibility for all the existing 1.x code.
The original proposal also required that each core have a directory in the library tree for core specific code.
Several of us pushed that this was unworkable as each core needs to be able to release and maintain its own core specific library that is independent of any other version of that library. After a few IDE releases the core specific directory within a library was effectively dropped as the arduino team realized that their original proposal was unworkable and now a library can exist in multiple places and specify what cores it works on. (They saw the light as they began developing and doing maintenance for DUE)
This allows a library to be in the sketchbook/libraries area and specify which cores it works on, or be shipped with a core for a version of the library that works with that core.
This is the way you want it. That way, a 3rd party core can ship its own h/w specific version of the library that gets used when code is built for boards that use that core.
i.e. if building for UNO, the avr Wire library in the arduino avr core is use.
If building for esp8266 their Wire library is used, if building for Teensy the teensy Wire library is used and if building for teensy 3x the teensy3x library is used, etc...
So yes you can and will have certain libraries that show up in multiple places.
This is normal and is what makes things work for different cores.
The IDE will automatically detect and use the proper library for the core.
These types of libraries are the core specific libraries, for example: Wire, SPI, SoftwareSerial, EEPROM
Where things can get messy or break is when using your personal sketchbook/libraries area.
So this comment is of concern:
- Pick and choose ONLY the Libraries I ever use and put them inside my sketch folder.
Not sure if you meant sketch folder or sketchbook/libraries folder.
I haven't followed if the IDE now allows libraries to be in the actual directory with the sketch, which it sounds like what you might doing.
If so, the key thing to remember is that in those cases, not to bundle core specific libraries as those will be in the core that the code is being built for.
i.e. don't provide libraries like Wire, SPI etc... Let the IDE use the one that comes with the core.
The sketchbook libraries (and I'm guessing sketch libraries if that is now supported) trump other library areas, so you don't want to use it for core specific libraries since that area can be used on all cores.
For example, If you have a library that says it works on all cores but really doesn't,
that can create a library that gets used for a core that doesn't work or perhaps doesn't even compile.
But that typically doesn't cause duplicate library messages.
Those usually are spit out by the IDE when there are multiple libraries of equal priority installed in different directory names. i.e. you have a library called "foo" that has header called "foo.h" and the code for that library is installed in two different places, perhaps in directory called "foo" and "foo2" etc...
I'm not sure what is going on with your system/environment, as you have not provided quite a bit of information.
i.e. IDE version, where it is installed, where your sketchbook is located, and what libraries have been installed in which locations.
And a full sketch directory tree of a sketch that is having these issues.