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What is Git Submodule workflow for projects with modules which located in many directories?

This screen describes what exactly I need http://gyazo.com/6c4a6f8d5ed19a9e80abd4b101675cb5 or good description in like Git submodule or sub-repository or remote?.

Every module/theme/plugin have separate repository/subrepository.

But problem is when module located in different directories(related problem desctibes in Best practices for using Git with Magento?) I tried did it with Modgit-git-plugin, BUT

1) I'm not sure that is the best solution for this problem. Guys what do you think? 2) I can't synchronize modgit source folder with module and files in root of site, for example, see my actions: A. modgit clone magento-turpentine https://github.com/nexcess/magento-turpentine.git

I get: (A-files) module

          shell/*
          app/etc/modules/*
          app/code/community/*
          app/code/local/Mage/Core/Model/S*
          app/design/adminhtml/default/default/template/turpentine/*

(B-files) .modgit/magento-turpentine/source/

          .modgit/magento-turpentine/source/shell/*
          .modgit/magento-turpentine/source/app/etc/modules/*
          .modgit/magento-turpentine/source/app/code/community/*
          .modgit/magento-turpentine/source/app/code/local/Mage/Core/Model/S*
          .modgit/magento-turpentine/source/app/design/adminhtml/default/default/template/turpentine/*

B. modgit update-all

C. Than I create new remote repository and pushed cd .modgit/magento-turpentine/source/ git remote add origin git@bitbucket.org:myteam/magento-turpentine-test.git git push -u origin master

I have two programmers, 1st work with (A-files) 2nd work with (B-Files)(only with this git@bitbucket.org:myteam/magento-turpentine-test.git repository) What is the right methods synchronize files in root(main repository) and .modgit/module/source/.git... repository?

Conclusions: 1) I'm not sure that is the best solution for this problem. Guys what do you think? 2) I can't synchronize modgit(details above), please help.

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