Best practices for change management

I am trying to find best practices regarding a concept related to change management in databases, only storing parts that have changed.

Our project involves storing a versioned dependency graph whenever a build takes place. Since the dependencies can grow very quickly we want to optimize how they are stored and only save the dependencies that are actually being changed. So let´s say we have BuildA where the whole dependency graph is created. When we create BuildB where only dep3 is changed we would only like to store dep3 but reference the other dependencies from BuildA

BuildA (Version1)
   SolutionA
      dep1
      dep2
      dep3

BuildB (Version2)
      dep3

Is there any best practices when optmizing change history. E.g. Source Code management or something similar?