Main project script sets executable flags at configure time

Until now, when the project's source was downloaded from something like
arXiv, in `README.md', we were instructing them to set the executable flags
of all the files that need it. But except for `./project', the reader
shouldn't have to worry about the project internals! Once its executable,
`./project' can easily fix the executable flags of all the files that need
it automatically.

With this commit, in `README.md', we just instruct the reader to set the
executable flag of `./project' and any other file that needs an executable
flag is given one at the start of the set of commands for `./project
configure'. In customized projects, if an author needs executable flags on
any other files, they can easily add it there without involving the user.

3 files changed, 23 insertions, 3 deletions

diff --git a/.file-metadata b/.file-metadata
index b75a1d7..196f109 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/README.md b/README.md
index 3dd2757..f0f6acc 100644
--- a/README.md
+++ b/README.md
@@ -112,11 +112,11 @@ this source from arXiv, some minor extra steps are necessary:
 
 2. arXiv removes the executable flag from the files (for its own
    security). So before following the standard procedure of projects
-   described in the sections above, its necessary to make the necessary
-   script files executable with the command below:
+   described in the sections above, its necessary to set the executable
+   flag of the main project management file with this command:
 
      ```shell
-     $ chmod +x project reproduce/software/bash/* reproduce/analysis/bash/*
+     $ chmod +x project
      ```
 
 3. Remove extra files. In order to make sure arXiv can build the paper
diff --git a/project b/project
index 383ecb1..14fc272 100755
--- a/project
+++ b/project
@@ -21,6 +21,10 @@
 # Stop the script if there are any errors.
 set -e
 
+
+
+
+
 # Default option values
 jobs=0     # 0 is for the default for the `configure.sh' script.
 group=
@@ -223,6 +227,22 @@ case $operation in
     # Build the project's software.
     configure)
 
+        # Set executable flags
+        # --------------------
+        #
+        # In some scenarios (for example when using a tarball from arXiv),
+        # it may happen that the host server has removed the executable
+        # flags of all the files. In `README.md' we instruct the readers on
+        # setting the executable flag of this script. But we don't want the
+        # 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/bash/* 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
         # allow the configuration to complete).