Top level READMEs renamed to be similar to actual project

Until now, were were advising the users to rename the two README files
after cloning the project. This was because online Git browsers usually
display the `README.md' file, so we wanted the description of the pipeline
to be visible in the pipeline, and later when a project adopts it, they can
have their own `README.md'. But the problem is that any change in
`REAME.md' will later cause conflicts with a project's `README.md'. So we
are now using the same naming convention as the papers that use the
pipeline.

1 files changed, 0 insertions, 76 deletions

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-Reproduction pipeline for paper XXXXXXX
-=======================================
-
-This is the reproduction pipeline for the paper titled "**XXXXXX**", by
-XXXXXXXX et al. (**IN PREPARATION**).
-
-A *reproduction pipeline* contains the full instructions to configure and
-build the necessary software packages used in the analysis, and uses them
-*exactly* reproduce what we have published. All the scripts/instructions
-are in a human *and* computer readable format (scripts and Makefiles).
-
-The only dependency for the pipeline is **Wget**, and a minimal Unix-based
-building environment including a C compiler (already available on your
-system if you have ever installed a software from source). Note that **Git
-is not mandatory**: if you don't have Git to run the first command below,
-go to the URL given in the command on your browser, and download them
-manually (there is a button to download a compressed tarball of the
-project).
-
-```shell
-$ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-$ ./configure
-$ .local/bin/make -j8
-```
-
-For a general introduction to reproducible science as implemented in this
-pipeline, please see the [principles of reproducible
-science](http://akhlaghi.org/reproducible-science.html), and a
-[reproducible paper
-template](https://gitlab.com/makhlaghi/reproducible-paper) that is based on
-it.
-
-
-
-Running the pipeline
---------------------
-
-This pipeline was designed to have as few dependencies as possible.
-
-1. Necessary dependencies:
-
-   1.1: Minimal software building tools like C compiler, Make, and other
-        tools found on any Unix-like operating system (GNU/Linux, BSD, Mac
-        OS, and others). All necessary dependencies will be built from
-        source (for use only within this pipeline) by the `./configure'
-        script (next step).
-
-   1.2: (OPTIONAL) Tarball of dependencies. If they are already present (in
-        a directory given at configuration time), they will be
-        used. Otherwise, *GNU Wget* will be used to download any necessary
-        tarball. The necessary tarballs are also collected in the link
-        below for easy download:
-
-          https://gitlab.com/makhlaghi/reproducible-paper-dependencies
-
-2. Configure the environment (top-level directories in particular) and
-   build all the necessary software for use in the next step. It is
-   recommended to set directories outside the current directory. Please
-   read the description of each necessary input clearly and set the best
-   value. Note that the configure script also downloads, builds and locally
-   installs (only for this pipeline, no root previlages necessary) many
-   programs (pipeline dependencies). So it may take a while to complete.
-
-     ```shell
-     $ ./configure
-     ```
-
-3. Run the following command (local build of the Make software) to
-   reproduce all the analysis and build the final `paper.pdf` on *8*
-   threads. If your CPU has a different number of threads, change the
-   number (you can see the number of threads available to your operating
-   system by running `./.local/bin/nproc`)
-
-     ```shell
-     $ .local/bin/make -j8
-     ```