Updated Installation instructions (rest => markdown)

Installation-instructions.md

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+## 1) Setup the environment::
+
+`$ ./configure <config_file> (--production | --development)`
+
+For example you can type `./configure config/gfortran.cfg --production`
+
+This command have to purpose :
+
+ - Download and install all the requirements.
+   Installing OCaml and the Core library may take some time (up to 20min on an old machine).
+ - And create the file which contains all the tree dependencies for the binaries.  
+   It's not a Makefile, but a Ninja file (so don't type `make` is hopeless, type `ninja` instead)
+
+By default, the Ocaml compiler will be installed in ``$HOME/.opam``. 
+For more info about the Ocaml installation, check the Opam website :
+https://opam.ocaml.org/doc/Install.html
+
+####Compilation Flags (`<config_file>`)
+
+`<config_file>` is the path to the file who contain all the flags useful for the compilation:  like the optimization flags, the Lapack libary, etc.  We have two default configure file in  ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``.  You can edit these files to modify the compiling options. 
+
+Note that the ``popcnt`` instruction accelerates *a lot* the programs, so the
+SSE4.2, AVX or AVX2 instruction sets should be enabled if possible.
+
+If you encounter an error saying that your Fortran compiler can't produce
+executables, it means that the program was built using an instruction set
+not supported by the current processor. In that case, use the ``-ax`` option
+of the Intel Fortran compiler instead of the ``-x`` option, or the
+``-march=native`` option of gfortran.
+
+#### What utilization of the code will you do?
+
+* If you only want the binaries (for production workflow) use the flag
+  `--production` in when calling this script. It's quicker 
+* Else if you are a developer and you want to be able to compile specific modules use: `--development`. It will create for you the `build.ninja` in each module
+
+### 2) Set environment variable
+A configuration file named ``quantum_package.rc`` will be created.
+To finish the installation, source this file in your shell::
+
+    `source quantum_package.rc`
+
+And you can also source it inside your ``.bashrc`` file.
+
+If you use a C-shell, you will have to translate the ``.bashrc`` file into
+C-shell syntax and source it in your shell.
+
+### Optional) Add some new module
+
+From speed consideration, the quantum package have no executable out of the box. You need to install (and then compile) some module, if you wan't the executable ; the `qp_module.py` will help you.
+
+```
+      Usage: qp_module.py list (--installed|--avalaible-local|--avalaible-remote)
+       qp_module.py install <name>...
+       qp_module.py create -n <name> [<children_module>...]
+       qp_module.py download -n <name> [<path_folder>...]
+```
+
+ For exemple you can type : `qp_module.py install Full_CI`. This will install the `Full_CI` module. All the module installed a in the `$QP_ROOT/src/` if you wan't to check it.
+
+### 3) Compiling the fortran
+
+Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
+
+If you have set the `--developement` flag in a specific module you can go in
+the corresponding module `$QP_ROOT/src/module_name`- directory and run `ninja` to build only this module.
+You can type `ninja all` in a module for compiling all the submodule
+
+### 4) Compiling the OCaml
+You need to compile the OCaml source code. OCaml as here to handle the hight level IO.
+```
+    cd $QP_ROOT ; make -C ocaml/
+```
+
+### 5) Testing if all is ok
+Some unit test are available in the `test` directory. For runing the test 
+```
+ cd $QP_ROOT/tests
+ bats bats/qp.bats
+```

Installation-instructions.rest

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-Setup the environment::
-
-    ./setup_environment.sh
-
-This will automatically download and compile the requirements. 
-
-By default, the Ocaml compiler will be installed in ``$HOME/.opam``. 
-For more info about the Ocaml installation, check the Opam website :
-https://opam.ocaml.org/doc/Install.html
-
-A configuration file named ``quantum_package.rc`` will be created.
-To finish the installation, source this file in your shell::
-
-    source quantum_package.rc
-
-And you can also source it inside your ``.bashrc`` file.
-
-If you use a C-shell, you will have to translate the ``.bashrc`` file into
-C-shell syntax and source it in your shell.
-
-Finally, create the ``Makefile.config`` file from the ``Makefile.config.example``.
-Note that the ``popcnt`` instruction accelerates *a lot* the programs, so the
-SSE4.2, AVX or AVX2 instruction sets should be enabled if possible.
-
-If you encounter an error saying that your Fortran compiler can't produce
-executables, it means that the program was built using an instruction set
-not supported by the current processor. In that case, use the ``-ax`` option
-of the Intel Fortran compiler instead of the ``-x`` option, or the
-``-march=native`` option of gfortran.
-
-Finally, build the binary files ::
-
-    make build
-