Libraries under version control

Projects General Guidance
1

Hi everyone,
I'm looking for some easy way to keep my libraries accessible to many projects and be integrated into version control (separate of projects).
Some of the libraries are mine, and some are modified versions of libraries found on the internet.
They are meant to be shared between projects, so I don't want to copy them to each project that uses them, but need to have them under version control.

Previously I kept them in a separate project that was under version control, and I had directory junctions in Arduino's library folder pointing to the specific libraries.

However since some recent Arduino version (in 1.6.6 it wasn't working, now I'm using 1.6.7) this approach stopped working. Arduino IDE now does some checking that seems to be aware of the links and fails to compile project. Now it doesn't work with both directory junctions and ntfs symbolic links.
For example I get this during compilation:

readlink C:\Users\Mikaka\Documents\Arduino\libraries\AESLib: The system cannot find the file specified.

Compilation error.

Is there a way to override this behavior in IDE? Or is there some other way keep my modified libs under version control?
I was thinking about making a Documents\Arduino\libraries folder a git repository. But I don't know if it won't interfere with Arduino IDE (Git would keep hidden folders inside library folder).

Thanks in advance, any help is appreciated.

2

Untested: I'd try git, with the (master) repository in some unrelated place, from where you can check out the libraries into any number of IDE version directories. SVN may work as well. The hidden folders should not cause trouble, find out yourself.

3

I will be interested to see if there is a simple solution to this.
I have recently developed my own system to enable me to reproduce the exact program that exists in an Arduino / Atmel MCU - but I have never used Git or SVN.

What do you mean by "I had directory junctions in Arduino's library folder pointing to the specific libraries"?

What operating system is on your PC?

...R