Drupal - Drush Make removes .git folders

Pass the "--working-copy" switch to Drush Make.

drush make --working-copy site.make

And if you're using YAML for your make file, the following will allow you to preserve the .git repository info:

projects:

  drupal:
    type: core
    version: 8.0.x
    download:
      working-copy: true

And further, if you don't want drush to add in extra information to projects' .info files, make sure you use the --no-gitinfofile option when running drush make.

On project by project basis, in a make file you can add the option like this

projects[project_name][download][type] = git
projects[project_name][download][url] = ssh://[email protected]
projects[project_name][options][working-copy] = TRUE