doc on git commands

doc/git commands.md

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+Guidelines to develop the ontology with Git and Github
+==========================================================
+
+## Settings up your account on Github
+
+### Create an account
+
+### Add a public ssh key
+
+## Installing Git on your computer
+
+https://git-scm.com/downloads
+
+
+## Interacting with the repository remotely
+
+In our collaborative work, we aim at developing the ontology in parallel.
+Each participant has a local repository to make its development. The local
+developments are then pushed to the remote repository to be available for all the partners.
+
+The main operations are described in the following sections.
+
+### Clone the repository
+
+The current version is available on GitHub so we want to copy that repository locally
+to make our changes.
+We will ***clone the repository*** with the following command line:
+```
+git clone [email protected]:emmo-repo/domain-microstructure.git
+```
+
+This operation uses ssh protocols so you need to have stored your public ssh key in your profile.
+It is possible to clone also with https but it is simpler with ssh.
+
+After that operation, you have the copy of the default branch (*main* in our case) 
+but also all the branches.
+
+### Transfer changes to the remote repository
+
+Git aims at tracking the changes between version. For that reason, when you have made 
+some changes two operations are needed: tagging and committing. Tagging will consist
+in indicating which file is to be marked as changed (and so which changes will be recorded
+in the repository). Committing will actually do the recording of the changes.
+
+Tagging is done by: ```git add name_of_file```
+
+Commiting is done by:  ```git commit -m "my description of the changes" ```
+
+The command ```git status``` will give you an overview of the tracked files that 
+have been modified, the tagged files, and also of the files that are not tracked.
+It also indicates on which branch you are.
+
+After the commit, your local repository has been updated. This update needs to 
+be transferred to the remote repository stored on GitHub. We need to push the changes
+by:
+```git push```
+
+### Update your local repository
+
+```git fetch``` The git fetch command downloads commits from the remote repository
+into your local repository to see the changes.
+
+```git pull``` The git pull command is used to fetch and download content from a remote repository
+and immediately update the local repository to match that content. 
+
+To avoid merging issues, it is important to pull from the remote repository before 
+adding new changes.
+
+### Branching
+
+Significant modifications on the code are usually done in branches. When the new feature of
+the branch is developed, the branch can be merged with the main branch.
+
+<p align="center"><img src="branching diagram.png" width="600"></p>
+
+The main commands are:
+
+```git branch ``` to get the list of branches.
+
+```git checkout name_of_branch ``` to change to an existing branch.
+
+```git checkout -b name_of_branch ``` to create a new branch and change to it.
+
+```git checkout -b name_of_branch ``` to create a new branch and change to it.
+
+
+### Merging
+
+```git merge name_of_branch``` to merge the branch with your current branch.
+
+In case of conflicts between your changes and what has been changed since your latest
+update from the remote repository, you will need to resolve the conflicts.
+During merge, the files will be modified to contain both versions of the portions
+of codes. You need then to select what to keep.
+
+More details are available here: 
+https://www.atlassian.com/git/tutorials/using-branches/merge-conflicts
+
+
+
+
+
+
+