How to exclude some directories (and their contents) on pull request?

Hello,

We have many sites using the same bitbucket repository. But some files differ between the sites, so we just put them into specifical directories. And all thoses specificals directories are comitted in the repository. In our production server, I would like to get only the directory corresponding to one site. 

I tried to add the path in .git/info/exclude file, but it isn't working.

I tried also with git update-index --skip-worktree, but it only accept files and not directory (as some files could be add later, I need to exclude directories).

To be sure to be clear:

We have 2 sites (A and B) with almost the same codes. We have 2 directories (A and B) wich contains the specifical files. On the site A, I wish to get only directory A when I pull the sources, and only directory B on site B.

Do you have a solution to do this?

thank you in advance,

Yann