Single wrapper instead of old ./configure, Makefile and ./for-group

Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.

This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).

With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:

   $ ./project configure
   $ ./project make

To work on the project with other users in a group these commands can be
used:

  $ ./project configure --group=GROUPNAME
  $ ./project make      --group=GROUPNAME

The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:

  $ ./project configure -e --host-cc
  $ ./project make -j8

The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.

On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).

This fixes bug #56682.

1 files changed, 6 insertions, 6 deletions

diff --git a/README.md b/README.md
index 212e178..bb46fe0 100644
--- a/README.md
+++ b/README.md
@@ -19,8 +19,8 @@ a compressed tarball of the project).
 
 ```shell
 $ git clone XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-$ ./configure
-$ .local/bin/make -j8
+$ ./project configure
+$ ./project make -j8
 ```
 
 For a general introduction to reproducible science as implemented in this
@@ -44,8 +44,8 @@ This project was designed to have as few dependencies as possible.
    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 project) by the `./configure'
-        script (next step).
+        source (for use only within this project) by the `./project
+        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
@@ -69,7 +69,7 @@ This project was designed to have as few dependencies as possible.
    programs (project dependencies). So it may take a while to complete.
 
      ```shell
-     $ ./configure
+     $ ./project configure
      ```
 
 3. Run the following command (local build of the Make software) to
@@ -79,7 +79,7 @@ This project was designed to have as few dependencies as possible.
    system by running `./.local/bin/nproc`)
 
      ```shell
-     $ .local/bin/make -j8
+     $ ./project make -j8
      ```