Checklist modified to keep pipeline history

Until now, in the check list of `README.md', we were recommending to delete
the history of the pipeline and start your own history from that. But this
disables users of the pipeline to keep it up to date with new features that
are added to it.

With this commit, the main branch is now called `pipeline' (to allow users
to use `master' for their own research) and in the clone command, the
pipeline's remote is now called `pipeline-origin' (to allow the user to use
`origin' for their own remote).

1 files changed, 55 insertions, 34 deletions

diff --git a/README.md b/README.md
index 8ecbc02..a972258 100644
--- a/README.md
+++ b/README.md
@@ -382,13 +382,26 @@ to see if everything works correctly before expanding it. If you notice
 anything missing or any in-correct part (probably a change that has not
 been explained here), please let us know to correct it.
 
- - **Get this repository** (if you don't already have it): Arguably the
-     easiest way to start is to clone this repository as shown below:
+As described above, the concept of a reproduction pipeline heavily relies
+on [version
+control](https://en.wikipedia.org/wiki/Version_control). Currently this
+pipline uses Git as its main version control system. If you are not already
+familiar with Git, please read the first three chapters of the [ProGit
+book](https://git-scm.com/book/en/v2) which provides a wonderful practical
+understanding of the basics. You can read later chapters as you get more
+advanced in later stages of your work.
+
+ - **Get this repository and its history** (if you don't already have it):
+     Arguably the easiest way to start is to clone this repository as shown
+     below. The main branch of this pipeline is called `pipeline`. This
+     allows you to use the common branch name `master` for your own
+     research, while keeping up to date with improvements in the pipeline.
 
      ```shell
-     $ git clone https://gitlab.com/makhlaghi/reproducible-paper.git
+     $ git clone --origin pipeline-origin https://gitlab.com/makhlaghi/reproducible-paper.git
      $ mv reproducible-paper my-project-name
      $ cd my-project-name
+     $ git checkout -b master
      ```
 
  - **Copyright**, **name** and **date**: Go over the existing scripting
@@ -496,49 +509,57 @@ been explained here), please let us know to correct it.
      - Delete the following files: `README.md`, all `delete-me*` files (in
        `reproduce/config/pipeline`, `reproduce/src/make`, and `tex`).
 
- - **Initiate a new Git repo**: You probably don't want to mix the history
-     of this template reproduction pipeline with your own reproduction
-     pipeline. You have already made some small changes in the previous
-     step, so let's re-initiate history before continuing. But before doing
-     that, keep the output of `git describe` in a place and write it in
-     your first commit message to document what point in this pipeline's
-     history you started from. Since the pipeline is highly integrated with
-     your particular research, it may not be easy to merge the changes
-     later. Having the commit information that you started from, will allow
-     you to check and manually apply any changes that don't interfere with
-     your implemented pipeline. After this step, you can commit your
-     changes into your newly initiated history as you like.
+ - **Your first commit**: You have already made some small and basic
+     changes in the steps above and you are in the `master` branch. So, you
+     can officially make your first commit in your project's history. But
+     before that you need to make sure that there are no problems in the
+     pipeline (this is a good habit to always re-build the system before a
+     commit to be sure it works as expected).
 
      ```shell
-     $ git describe          # The point in this history you started from.
-     $ git clean -fxd        # Remove any possibly created extra files.
-     $ rm -rf .git           # Completely remove this history.
-     $ git init              # Initiate a new history.
-     $ git add --all         # Stage everything that is here.
-     $ git commit            # Your first commit (mention the first output).
+     $ make clean            # Clean already built pipeline outputs.
+     $ make                  # Build the pipeline to ensure everything is fine.
+     $ git add --all         # Stage all the changes.
+     $ git commit            # Your first commit, add a nice description.
      $ git tag -a v0         # Tag this as the zero-th version of your pipeline.
      ```
 
- - **Notice on reproducibility**: Add a notice somewhere prominent in the
-     first page within your paper, informing the reader that your research
-     is fully reproducible. For example in the end of the abstract, or
-     under the keywords with a title like "reproducible paper". This will
-     encourage them to publish their own works in this manner also and also
-     will help spread the word.
+ - **Remote repository**: You can use any [hosting
+     facility](https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities)
+     you prefer to keep an online copy of your project's version controlled
+     history. We recommend [GitLab](https://gitlab.com) because it allows
+     hosting of unlimited number of private repositories (necessary in many
+     cases prior to publishing a result) for free and because you can host
+     GitLab on your own server. Create an account in your favorite service
+     (if you don't already have one) and define a new project there. It
+     will give you a link that you can put in place of `XXX` in the command
+     below.
+
+     ```shell
+     git remote add origin XXX
+     git push -u origin --all
+     git push -u origin --tags
+     ```
 
  - **Start your exciting research**: You are now ready to add flesh and
      blood to this raw skeleton by further modifying and adding your
      exciting research steps. You can use the "published works" section in
-     the introduction as some fully working models to learn from.
+     the introduction as some fully working models to learn from. Also,
+     don't hesitate to contact us if you have any questions.
+
+ - **Pre-publication: add notice on reproducibility**: Add a notice
+     somewhere prominent in the first page within your paper, informing the
+     reader that your research is fully reproducible. For example in the
+     end of the abstract, or under the keywords with a title like
+     "reproducible paper". This will encourage them to publish their own
+     works in this manner also and also will help spread the word.
 
  - **Feedback**: As you use the pipeline you will notice many things that
      if implemented from the start would have been very useful for your
-     work. This can be in the actual file structure of the pipeline or in
-     useful implementation and usage tips like below. In any case, since
-     this concept is still evolving, please share your thoughts and
-     suggestions, so we can add them here for everyone's benefit.
-
-
+     work. This can be in the actual scripting and architecture of the
+     pipeline or in useful implementation and usage tips, like those
+     below. In any case, please share your thoughts and suggestions with
+     us, so we can add them here for everyone's benefit.