IMPORTANT: Project preparation is now also done with project make

Until now, the main commands to run the project were these: `./project
configure' (to build the software), `./project prepare' (to possibly
arrange input datasets and build special configuration Makefiles) and
finally `./project make' to run the project.

The main logic behind the "prepare" phase `top-prepare.mk' is to build
configuration files that can be fed into the "make" step and optimize its
operation. For example when the total number of necessary inputs for the
majority of the analysis is not as large as the total number of
inputs. With "prepare" (when necessary), you go through the raw inputs,
select the ones that are necessary for the rest of the project. The output
of `top-prepare.mk' is a configuration file (a Make variable) that keeps
the IDs (numbers, names, etc). That configuration file would then be used
in the `top-make.mk' to identify the lower level targets and allow optimal
project organization and management.

But the last two are both part of the analysis, and while they indeed need
different calls to Make to be executed, many projects don't actually need a
preparation phase: ultimately, its an implementation choice by the project
developers and doesn't concern the project users (or the developers when
they are running it).

To avoid confusing the users, or simply annoying them when a projet doesn't
need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk'
Makefiles are called with the single `./project make' command and
`./project prepare' has been dropped. I noticed this while writing the
paper on this system.

1 files changed, 1 insertions, 15 deletions

diff --git a/README.md b/README.md
index 3796d2f..f89f89a 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,6 @@ received this source from arXiv, please see the respective section below.
 $ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 $ cd XXXXXXXXXXXXXXXXXX
 $ ./project configure
-$ ./project prepare
 $ ./project make
 ```
 
@@ -77,20 +76,7 @@ requiring root/administrator permissions.
      $ ./project configure
      ```
 
-3. In some cases, the project's analysis may need some preparations to
-   optimize its processing. This is usually mainly related to input data,
-   and some very basic calculations that can help the management of the
-   overall lproject in the main/next step. To do the basic preparations,
-   please run this command to do the preparation 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
-     $ ./project prepare -j8
-     ```
-
-4. Run the following command to reproduce all the analysis and build the
+3. Run the following command 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`)