i.e. Do you put the whole package under VCS or just the components you are programming? Packages by there nature will get upgraded and that code will need to be added into the VCS, plus there is a lot of code that is static.
Specifically I am going to be working on Joomla, adding and building modules, customising modules and the look and feel. Initially this will be just me but will expand to possibly two more developers as the project ramps up. My reaction would be just to VCS the lot, it means that i know it is all there and deployment via CI is easier(?).
The alternative is to exclude the bulk of the code that is not being altered which could be error prone and laborious.
As there is not a specific answer for this and i am looking for either experience or best practice advice i have marked it community wiki.