Text surrounding software acknowledgements as a configuration file

Until now, the English texts that embeds the list of software to
acknowledge in the paper was hard-wired into the low-level coding
('reproduce/software/shell/configure.sh' to be more specific). But this
file is very low-level, thus discouraging users to modify this surrounding
text.

While the list of software packages can be considered to be 'data' and is
fixed, the surrounding text to describe the lists is something the authors
should decide on. Authors of a scientific research paper take
responsibility for the full paper, including for the style of the
acknowledgments, even if these may well evolve into some standard text.

With this commit, authors who do *not* modify
'reproduce/software/config/acknowledge_software.sh' will have a default
text, with only a minor English correction from earlier versions of
Maneage. However, Authors choosing to use their own wording should be able
to modify the text parameters in
`reproduce/software/config/acknowledge_software.sh` in the obvious
way. This is much more modular than asking project authors to go looking
into the long and technical 'configure.sh' script.

Systematic issues: the file
`reproduce/software/config/acknowledge_software.sh` is an executable shell
script, because it has to be called by
`reproduce/software/shell/configure.sh`, which, in principle, does not yet
have access to `GNU make` (if I understand the bootstrap sequence
correctly). It is placed in `config/` rather than `shell/`, because the
user will expect to find configuration files in `config/`, not in `shell/`.

A possible alternative to avoid having a shell script as a configure file
would be to let `reproduce/software/config/acknowledge_software.sh` appear
to be a `make` file, but analyse it in `configure.sh` using `sed` to remove
whitespace around `=`, and adding other hacks to switch from `make` syntax
to `shell` syntax. However, this risks misleading the user, who will not
know whether s/he should follow `make` conventions or `shell` conventions.

1 files changed, 6 insertions, 5 deletions

diff --git a/project b/project
index cc2140f..728d488 100755
--- a/project
+++ b/project
@@ -324,11 +324,12 @@ case $operation in
         # user to have to worry about any other file that needs an
         # executable flag.
         #
-        # Basically, all the files (shell scripts) in the two
-        # `reproduce/*/bash' should need executable flags, so we are giving
-        # them executable flags by default. If any other file in your project
-        # needs such flags, add them here.
-        chmod +x reproduce/software/shell/* reproduce/analysis/bash/*
+        # Basically, all the project shell scripts need executable flags so
+        # to make sure they have them, we are activating the executable
+        # flags by default here every time './project configure' is run. If
+        # any other file in your project needs such flags, add them here.
+        chmod +x reproduce/software/shell/* reproduce/software/config/*.sh \
+              reproduce/analysis/bash/*
 
         # If the user requested, clean the TeX directory from the extra
         # (to-be-built) directories that may already be there (and will not