Imported recent work in Maneage, minor conflicts fixed

Only two small conflicts came up:

 * The addition of the hardware architecture macro in 'paper.tex' (which
   was removed for now, but will be added as the referee has requested
   within the text).

 * The usage of "" around directory variables in 'paper.mk'.

11 files changed, 362 insertions, 179 deletions

diff --git a/README.md b/README.md
index 748a791..24e12d8 100644
--- a/README.md
+++ b/README.md
@@ -249,21 +249,18 @@ MB), not the full TeXLive collection!
     ```
 
  2. **Maneage dependencies:** By default the "slim" versions of the
-    operating systems don't contain a compiler, so you need to use the
-    selected operating system's package manager to import them. You can
-    optionally install two other programs: 1) To inspect/edit the project's
-    source files later, install your favorite text editor. 2) If you don't
-    have the project's software tarballs, and want the project to download
-    them automatically, you also need a downloader.
+    operating systems don't contain a compiler (needed by Maneage to
+    compile precise versions of all the tools). You thus need to use the
+    selected operating system's package manager to import them (below is
+    the command for Debian). Optionally, if you don't have the project's
+    software tarballs, and want the project to download them automatically,
+    you also need a downloader.
 
     ```shell
     # C and C++ compiler.
     RUN apt-get update && apt-get install -y gcc g++
 
-    # Uncomment this to add a text editor (to modify source files later).
-    #RUN apt-get install -y nano
-
-    # Uncomment this if you don't have 'software-XXXX.tar.gz'
+    # Uncomment this if you don't have 'software-XXXX.tar.gz' (below).
     #RUN apt-get install -y wget
     ```
 
@@ -348,10 +345,14 @@ MB), not the full TeXLive collection!
 
  7. **Build the Docker image:** The `Dockerfile` is now ready! In the
     terminal, go to its directory and run the command below to build the
-    Docker image. Just set a `NAME` for your project and note that Docker
-    only runs as root.
+    Docker image. We recommend to keep the `Dockerfile` in **an empty
+    directory** and run it from inside that directory too. This is because
+    Docker considers that directories contents to be part of the
+    environment. Finally, just set a `NAME` for your project and note that
+    Docker only runs as root.
 
     ```shell
+    sudo su
     docker build -t NAME ./
     ```
 
@@ -407,6 +408,17 @@ docker container list
 docker commit XXXXXXX NEW-IMAGE-NAME
 ```
 
+#### Copying files from the Docker image to host operating system
+
+The Docker environment's file system is completely indepenent of your host
+operating system. One easy way to copy files to and from an open container
+is to use the `docker cp` command (very similar to the shell's `cp`
+command).
+
+```shell
+docker cp CONTAINER:/file/path/within/container /host/path/target
+```
+
 
 
 
diff --git a/paper.tex b/paper.tex
index c1d7b34..febd346 100644
--- a/paper.tex
+++ b/paper.tex
@@ -91,7 +91,6 @@ Data Lineage, Provenance, Reproducibility, Scientific Pipelines, Workflows
 
 
 
-
 % For peer review papers, you can put extra information on the cover
 % page as needed:
 % \ifCLASSOPTIONpeerreview
diff --git a/project b/project
index f696f26..4dc4bd1 100755
--- a/project
+++ b/project
@@ -167,27 +167,27 @@ do
 
 
   # Configure options:
-  -b|--builddir)         build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
-  -b=*|--build-dir=*)    build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
-  -b*)                   build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
-  -e|--existing-conf)    existing_conf=1;                                                          shift;;
+  -b|--build-dir)        IFS='"' build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
+  -b=*|--build-dir=*)    IFS='"' build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
+  -b*)                   IFS='"' build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
+  -e|--existing-conf)    existing_conf=1;                                                                  shift;;
   -e*|--existing-conf=*) on_off_option_error --existing-conf -e;;
-  --host-cc)             host_cc=1;                                                                shift;;
+  --host-cc)             host_cc=1;                                                                        shift;;
   --host-cc=*)           on_off_option_error --host-cc;;
-  -i|--input-dir)        input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
-  -i=*|--input-dir=*)    input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
-  -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//'); check_v "$1" "$input_dir";    shift;;
-  -m|--minmapsize)       minmapsize="$2";                            check_v "$1" "$minmapsize";   shift;shift;;
-  -m=*|--minmapsize=*)   minmapsize="${1#*=}";                       check_v "$1" "$minmapsize";   shift;;
-  -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//'); check_v "$1" "$minmapsize";   shift;;
-  -s|--software-dir)     software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
-  -s=*|--software-dir=*) software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
-  -s*)                   software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
-  --check-config)        check_config=1;                                                           shift;;
+  -i|--input-dir)        IFS='"' input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
+  -i=*|--input-dir=*)    IFS='"' input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
+  -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//');         check_v "$1" "$input_dir";    shift;;
+  -m|--minmapsize)       minmapsize="$2";                                    check_v "$1" "$minmapsize";   shift;shift;;
+  -m=*|--minmapsize=*)   minmapsize="${1#*=}";                               check_v "$1" "$minmapsize";   shift;;
+  -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//');         check_v "$1" "$minmapsize";   shift;;
+  -s|--software-dir)     IFS='"' software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
+  -s=*|--software-dir=*) IFS='"' software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
+  -s*)                   IFS='"' software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
+  --check-config)        check_config=1;                                                                   shift;;
   --check-config=*)      on_off_option_error --check-config;;
-  --clean-texdir)        clean_texdir=1;                                                           shift;;
+  --clean-texdir)        clean_texdir=1;                                                                   shift;;
   --clean-texdir=*)      on_off_option_error --clean-texdir;;
-  --all-highlevel)       all_highlevel=1;                                                          shift;;
+  --all-highlevel)       all_highlevel=1;                                                                  shift;;
   --all-highlevel=*)     on_off_option_error --all-highlevel;;
 
   # Configure and Make options:
@@ -279,7 +279,7 @@ EOF
             check=$(ls .local/version-info/proglib/)
             if ! [ "x$check" = x ]; then
                 printresults=1
-                ln -s $(pwd)/.local/version-info/proglib/* $checkdir/
+                ln -s "$(pwd)"/.local/version-info/proglib/* $checkdir/
             fi
 
             # If something was actually found, then print them.
@@ -304,7 +304,7 @@ EOF
         echo "========================"
 
         # Wait for the next round of checks.
-        sleep 1;
+        sleep 1
     done
     exit 0
 fi
@@ -506,22 +506,24 @@ case $operation in
         fi
 
         # Run the project's own shell without inheriting any environment
-        # from the host.
+        # from the host. The 'TERM' environment variable is necessary for
+        # tools like some text editors.
         bdir=`.local/bin/realpath .build`
-        instdir=$bdir/software/installed
+        instdir="$bdir"/software/installed
         .local/bin/env -i \
-                       HOME=$bdir \
+                       HOME="$bdir" \
+                       TERM="$TERM" \
                        CCACHE_DISABLE=1 \
-                       PATH=$instdir/bin \
-                       LDFLAGS=-L$instdir/lib \
-                       SHELL=$instdir/bin/bash \
-                       CPPFLAGS=-I$instdir/include \
-                       LD_LIBRARY_PATH=$instdir/lib \
+                       PATH="$instdir"/bin \
+                       LDFLAGS=-L"$instdir"/lib \
+                       SHELL="$instdir"/bin/bash \
+                       CPPFLAGS=-I"$instdir"/include \
+                       LD_LIBRARY_PATH="$instdir"/lib \
                        OMPI_MCA_plm_rsh_agent=/bin/false \
-                       PYTHONPATH=$instdir/lib/python/site-packages \
-                       PYTHONPATH3=$instdir/lib/python/site-packages \
+                       PYTHONPATH="$instdir"/lib/python/site-packages \
+                       PYTHONPATH3="$instdir"/lib/python/site-packages \
                        PS1="[\[\033[32m\](maneage)\[\033[00m\] \u@\h \W]$ " \
-                       $instdir/bin/bash
+                       "$instdir"/bin/bash
         ;;
 
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 2c08847..f363b6f 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -47,8 +47,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	@if [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" != x ]; then
 
           # Put a LaTeX input command for all the necessary macro files.
+          # 'hardware-parameters.tex' is created in 'configure.sh'.
 	  rm -f $(mtexdir)/project.tex
-	  for t in $(subst paper,,$(makesrc)); do
+	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
 	    echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex
 	  done
 	else
@@ -127,7 +128,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # do not use PGFPlots, then you should remove the `-shell-escape'
           # option for better security. See
           # https://savannah.nongnu.org/task/?15694 for details.
-	  latex -shell-escape -halt-on-error $$p/paper.tex
+	  latex -shell-escape -halt-on-error "$$p"/paper.tex
 	  bibtex paper
 
           # Hack: tidy up eprint+doi style that didn't work in .bst file.
@@ -143,7 +144,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 	    | sed -e 's/EOLINE/\n/g' > paper.bbl
 
           # The pre-final run of LaTeX after 'paper.bbl' was created.
-	  latex -shell-escape -halt-on-error $$p/paper.tex
+	  latex -shell-escape -halt-on-error "$$p"/paper.tex
 	fi
 
 
@@ -171,7 +172,7 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
           # See above for a warning and brief discussion on the the
           # pdflatex option `-shell-escape'.
-	  latex -shell-escape -halt-on-error $$p/paper.tex
+	  latex -shell-escape -halt-on-error "$$p"/paper.tex
 
           # Convert the DVI to PostScript, and the PostScript to PDF. The
           # `-dNOSAFER' option to GhostScript allows transparencies in the
@@ -182,6 +183,6 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
           # Come back to the top project directory and copy the built PDF
           # file here.
-	  cd $$p
+	  cd "$$p"
 	  cp $(texbdir)/$@ $(final-paper)
 	fi
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index b516a61..e7a0e63 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -44,6 +44,7 @@ make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba
 metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
 mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
 mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
+nano-checksum = d101e7f4802c079254e79340b433749dcd699fa9adec3f96e4218ec12f066a1f6b0954c27254bb6f019bc370ee2116817717870f4e2bc782c552442f2cc75195
 ncurses-checksum = 4c1333dcc30e858e8a9525d4b9aefb60000cfc727bc4a1062bace06ffc4639ad9f6e54f6bdda0e3a0e5ea14de995f96b52b3327d9ec633608792c99a1e8d840d
 openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34
 patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad
@@ -86,6 +87,7 @@ cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b74321
 cfitsio-checksum = 08a13931726b0ee15bd4e2ad6dd4debb8268f3b0bc33adadec5c6a29295dd536bcccb3cc949721c6cebac6f43b6118e5e38332ac0ba8a07a43553416d8debae5
 cmake-checksum = e0591d5fb234f3e7b74d6d2aad44fbf3e19e69547bd428681ba6ad0461d4f3d2a154605808b4733531d2c66f0e91eb39a179ae0d89a37e92a3f20e9cae691468
 eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972
+emacs-checksum = dfb26531d2c19cf9fb56505f03d799654b45e5f9528e777900e8280ed2c1d21e04c52f510528e31e015977c471ae63164cedee6174b7439ebcf479a21fc18064
 expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09
 fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38
 flex-checksum = b4ef58d4a1d66b213e2f59df06959decf46d26b253cdc3f51cd26e2e2b505461ef23dafa974dd2005b1f0cafa5a83fe9258baf78004b2fdae6dfc299bc17bfd1
@@ -130,6 +132,7 @@ swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b607
 swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb
 tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
 util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021
+vim-checksum = 06ba43386fcf308520d88d7a68e9bc1fabd824b05078b8f9112500a2ad4e50a91f1a1c2925889b7c06dbce34307f12abf508e2172b05fd283f965cc06552eb6d
 wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892
 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
 yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index 34c4d89..417f5ed 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -47,6 +47,7 @@
 #metastore-url = http://akhlaghi.org/maneage-software
 #mpc-url = http://ftp.gnu.org/gnu/mpc
 #mpfr-url = http://www.mpfr.org/mpfr-current
+#nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version)))
 #ncurses-url = http://ftp.gnu.org/gnu/ncurses
 #openssl-url = http://www.openssl.org/source
 #patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
@@ -88,6 +89,7 @@
 #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
 #cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv)
 #eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#emacs-url = http://ftp.gnu.org/gnu/emacs
 #expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
 #fftw-url = ftp://ftp.fftw.org/pub/fftw
 #flex-url = https://github.com/westes/flex/files/981163
@@ -133,6 +135,7 @@
 #tides-url = http://akhlaghi.org/maneage-software
 #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.35/
 #valgrind-url = https://sourceware.org/pub/valgrind
+#vim-url = ftp://ftp.vim.org/pub/vim/unix
 #wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib
 #xlsxio-url = https://github.com/brechtsanders/xlsxio/archive
 #yaml-url = pyyaml.org/download/libyaml
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 0a9e21e..0b3a4d2 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -44,6 +44,7 @@ make-version = 4.3
 metastore-version = 1.1.2-23-fa9170b
 mpc-version = 1.1.0
 mpfr-version = 4.0.2
+nano-version = 5.2
 ncurses-version = 6.2
 patchelf-version = 0.10
 perl-version = 5.32.0
@@ -94,6 +95,7 @@ cdsclient-version = 3.84
 cfitsio-version = 3.48
 cmake-version = 3.18.1
 eigen-version = 3.3.7
+emacs-version = 27.1
 expat-version = 2.2.9
 fftw-version = 3.3.8
 flex-version = 2.6.4-91-ga631f5d
@@ -134,6 +136,7 @@ swarp-version = 2.38.0
 swig-version = 3.0.12
 tides-version = 2.0
 util-linux-version = 2.35
+vim-version = 8.2
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5
 
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 0b672d8..934580a 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -56,8 +56,13 @@ ibdir   = $(BDIR)/software/installed/bin
 ildir   = $(BDIR)/software/installed/lib
 ibidir  = $(BDIR)/software/installed/version-info/proglib
 
-# Ultimate Makefile target.
-targets-proglib = low-level-links gcc-$(gcc-version)
+# Ultimate Makefile target. GNU Nano (a simple and very light-weight text
+# editor) is installed by default, it is recommended to have it in the
+# 'basic.mk', so Maneaged projects can be edited on any system (even when
+# there is no command-line text editor is available).
+targets-proglib = low-level-links \
+                  gcc-$(gcc-version) \
+                  nano-$(nano-version)
 all: $(foreach p, $(targets-proglib), $(ibidir)/$(p))
 
 # Define the shell environment
@@ -852,7 +857,8 @@ $(ibidir)/diffutils-$(diffutils-version): \
 $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
 	tarball=file-$(file-version).tar.gz
 	$(call import-source, $(file-url), $(file-checksum))
-	$(call gbuild, file-$(file-version), static,,V=1)
+	$(call gbuild, file-$(file-version), static, \
+	               --disable-libseccomp, V=1)
 	echo "File $(file-version)" > $@
 
 $(ibidir)/findutils-$(findutils-version): \
@@ -1145,11 +1151,22 @@ $(ibidir)/texinfo-$(texinfo-version): \
 	echo "GNU Texinfo $(texinfo-version)" > $@
 
 $(ibidir)/which-$(which-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=/which-$(which-version).tar.gz
+	tarball=which-$(which-version).tar.gz
 	$(call import-source, $(which-url), $(which-checksum))
 	$(call gbuild, which-$(which-version), static)
 	echo "GNU Which $(which-version)" > $@
 
+# GNU Nano is a very light-weight and small, command-line text editor (in
+# total around 3.5 Mb after installation!). It is top-level target in the
+# basic tools (nothing depends on it, it just depends on GCC). This is
+# because some projects may choose to not have it by manually removing it
+# from 'targets-proglib' above (it has no effect on processing after all!).
+$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
+	tarball=nano-$(nano-version).tar.xz
+	$(call import-source, $(nano-url), $(nano-checksum))
+	$(call gbuild, nano-$(nano-version), static)
+	echo "GNU Nano $(nano-version)" > $@
+
 
 
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 9f434bc..3c5e518 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -54,9 +54,9 @@ ibidir  = $(BDIR)/software/installed/version-info/proglib
 # Basic directories (specific to this Makefile).
 il64dir  = $(BDIR)/software/installed/lib64
 iidir    = $(BDIR)/software/installed/include
-shsrcdir = $(shell pwd)/reproduce/software/shell
-dtexdir  = $(shell pwd)/reproduce/software/bibtex
-patchdir = $(shell pwd)/reproduce/software/patches
+shsrcdir = "$(shell pwd)"/reproduce/software/shell
+dtexdir  = "$(shell pwd)"/reproduce/software/bibtex
+patchdir = "$(shell pwd)"/reproduce/software/patches
 itidir   = $(BDIR)/software/installed/version-info/tex
 ictdir   = $(BDIR)/software/installed/version-info/cite
 ipydir   = $(BDIR)/software/installed/version-info/python
@@ -449,6 +449,25 @@ $(ibidir)/eigen-$(eigen-version):
 	rm -rf $(ddir)/eigen-eigen-*
 	echo "Eigen $(eigen-version)" > $@
 
+# GNU Emacs is an advanced text editor (among many other things!), so it
+# isn't directly related to the analysis phase of a project. However, it
+# can be useful during the development of a project on systems that don't
+# have it natively. So probably after the project is finished and is ready
+# for publication, you can remove it from 'TARGETS.conf'.
+#
+# However, the full Emacs build has a very large number of dependencies
+# which aren't necessary in many scenarios so we are disabling everything
+# except the core Emacs functionality (using '--without-all') and we are
+# also disabling all graphic user interface features (using '--without-x').
+$(ibidir)/emacs-$(emacs-version):
+	tarball=emacs-$(emacs-version).tar.xz
+	$(call import-source, $(emacs-url), $(emacs-checksum))
+	$(call gbuild, emacs-$(emacs-version), static, \
+	               --without-all --without-x \
+	               --without-gnutls --with-ns=no, \
+	               -j$(numthreads) V=1)
+	echo "GNU Emacs $(emacs-version)" > $@
+
 $(ibidir)/expat-$(expat-version):
 	tarball=expat-$(expat-version).tar.lz
 	$(call import-source, $(expat-url), $(expat-checksum))
@@ -1374,8 +1393,30 @@ $(ibidir)/xlsxio-$(xlsxio-version): \
 	rm $(ibdir)/example_xlsxio_*
 	echo "XLSX I/O $(xlsxio-version)" > $@
 
-
-
+# VIM is a text editor which doesn't directly affect processing but can be
+# useful in projects during its development, for more see the comment above
+# GNU Emacs.
+$(ibidir)/vim-$(vim-version):
+	tarball=vim-$(vim-version).tar.bz2
+	$(call import-source, $(vim-url), $(vim-checksum))
+	cd $(ddir)
+	tar xf $(tdir)/$$tarball
+	n=$$(echo $(vim-version) | sed -e's|\.||')
+	cd $(ddir)/vim$$n
+	./configure --prefix=$(idir) \
+	            --disable-canberra \
+	            --enable-multibyte \
+	            --disable-netbeans \
+	            --disable-fontset \
+	            --disable-gpm \
+	            --disable-acl \
+	            --disable-gui \
+	            --with-x=no
+	make -j$(numthreads)
+	make install
+	cd ..
+	rm -rf vim$$n
+	echo "VIM $(vim-version)" > $@
 
 
 
@@ -1411,7 +1452,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	tar xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
 	sed -e's|@installdir[@]|$(idir)|g' \
-	    $$topdir/reproduce/software/config/texlive.conf \
+	    "$$topdir"/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
         # TeX Live's installation may fail due to any reason. But TeX Live
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 6ffb4ff..0d22dcc 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -48,7 +48,7 @@ need_gfortran=0
 # --------------------
 #
 # These are defined to help make this script more readable.
-topdir=$(pwd)
+topdir="$(pwd)"
 optionaldir="/optional/path"
 adir=reproduce/analysis/config
 cdir=reproduce/software/config
@@ -96,7 +96,8 @@ create_file_with_notice ()
 # an absolute address. With this function we can make sure of that.
 absolute_dir ()
 {
-    if stat "$1" 1> /dev/null; then
+    address="$1"
+    if stat "$address" 1> /dev/null; then
         echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
     else
         exit 1;
@@ -136,18 +137,18 @@ check_permission ()
 {
     # Make a `junk' file, activate its executable flag and record its
     # permissions generally.
-    local junkfile=$1/check_permission_tmp_file
-    rm -f $junkfile
-    echo "Don't let my short life go to waste" > $junkfile
-    chmod +x $junkfile
-    local perm_before=$(ls -l $junkfile | awk '{print $1}')
+    local junkfile="$1"/check_permission_tmp_file
+    rm -f "$junkfile"
+    echo "Don't let my short life go to waste" > "$junkfile"
+    chmod +x "$junkfile"
+    local perm_before=$(ls -l "$junkfile" | awk '{print $1}')
 
     # Now, remove the executable flag and record the permissions.
-    chmod -x $junkfile
-    local perm_after=$(ls -l $junkfile | awk '{print $1}')
+    chmod -x "$junkfile"
+    local perm_after=$(ls -l "$junkfile" | awk '{print $1}')
 
     # Clean up before leaving the function
-    rm -f $junkfile
+    rm -f "$junkfile"
 
     # If the permissions are equal, the filesystem doesn't allow
     # permissions.
@@ -187,8 +188,8 @@ check_permission ()
 free_space_warning()
 {
     fs_threshold=$1
-    fs_destpath=$2
-    return $(df $fs_destpath \
+    IFS='"' fs_destpath="$2"
+    return $(df "$fs_destpath" \
                 | awk 'FNR==2 {if($4>'$fs_threshold') print 1; \
                                else                   print 0; }')
 }
@@ -224,6 +225,62 @@ fi
 
 
 
+# Collect CPU information
+# -----------------------
+#
+# When the project is built, the type of a machine that built it also has
+# to to be documented. This way, if different results or behaviors are
+# observed in software-related or analysis-related phases of the project,
+# it would be easier to track down the root cause. So far this is just
+# later recorded as a LaTeX macro to be put in the final paper, but it
+# could be used in a more systematic way to optimize/revise project
+# workflow and build.
+hw_class=$(uname -m)
+if [ x$kernelname = xLinux ]; then
+    byte_order=$(lscpu \
+                     | grep 'Byte Order' \
+                     | awk '{ \
+                             for(i=3;i<NF;++i) \
+                             printf "%s ", $i; \
+                             printf "%s", $NF}')
+    address_sizes=$(lscpu \
+                     | grep 'Address sizes' \
+                     | awk '{ \
+                             for(i=3;i<NF;++i) \
+                             printf "%s ", $i; \
+                             printf "%s", $NF}')
+elif [ x$on_mac_os = xyes ]; then
+    hw_byteorder=$(sysctl -n hw.byteorder)
+    if   [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian";
+    elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian";
+    fi
+    address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical)
+    address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual)
+    address_sizes="$address_size_physical bits physical, "
+    address_sizes+="$address_size_virtual bits virtual"
+else
+    byte_order="unrecognized"
+    address_sizes="unrecognized"
+    cat <<EOF
+______________________________________________________
+!!!!!!!                 WARNING                !!!!!!!
+
+Machine byte order and address sizes could not be recognized. You can add
+the necessary steps in the 'reproduce/software/shell/configure.sh' script
+(just above this error message), or contact us with this web-form:
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    sleep 5
+fi
+
+
+
+
+
 # Check for C/C++ compilers
 # -------------------------
 #
@@ -717,7 +774,7 @@ fi
 
 # Build directory
 # ---------------
-currentdir=$(pwd)
+currentdir="$(pwd)"
 if [ $rewritepconfig = yes ]; then
     cat <<EOF
 
@@ -746,7 +803,7 @@ directory). The build directory cannot be a subdirectory of the source.
 EOF
     bdir=
     junkname=pure-junk-974adfkj38
-    while [ x$bdir = x ]
+    while [ x"$bdir" = x ]
     do
         # Ask the user (if not already set on the command-line).
         if [ x"$build_dir" = x ]; then
@@ -761,31 +818,31 @@ EOF
         fi
 
         # If it exists, see if we can write in it. If not, try making it.
-        if [ -d $build_dir ]; then
-            if mkdir $build_dir/$junkname 2> /dev/null; then
+        if [ -d "$build_dir" ]; then
+            if echo "test" > "$build_dir"/$junkname ; then
+                rm -f "$build_dir"/$junkname
                 instring="the already existing"
-                bdir=$(absolute_dir $build_dir)
-                rm -rf $build_dir/$junkname
+                bdir="$(absolute_dir "$build_dir")"
             else
                 echo " ** Can't write in '$build_dir'";
             fi
         else
-            if mkdir $build_dir 2> /dev/null; then
+            if mkdir "$build_dir" 2> /dev/null; then
                 instring="the newly created"
-                bdir=$(absolute_dir $build_dir)
+                bdir="$(absolute_dir "$build_dir")"
             else
                 echo " ** Can't create '$build_dir'";
             fi
         fi
 
-        # If its given, make sure it isn't a subdirectory of the source
+        # If it is given, make sure it isn't a subdirectory of the source
         # directory.
         if ! [ x"$bdir" = x ]; then
             if echo "$bdir/" \
-                    | grep '^'$currentdir 2> /dev/null > /dev/null; then
+                    | grep '^'"$currentdir" 2> /dev/null > /dev/null; then
 
                 # If it was newly created, it will be empty, so delete it.
-                if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
+                if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
 
                 # Inform the user that this is not acceptable and reset `bdir'.
                 bdir=
@@ -793,10 +850,30 @@ EOF
             fi
         fi
 
-	# If everything is fine until now, see if we're able to manipulate
-	# file permissions.
+        # If things are fine so far, make sure it does not contain a space
+        # or other meta-characters which can cause problems during software
+        # building.
+        if ! [ x"$bdir" = x ]; then
+            hasmeta=0;
+            case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac
+            if [ $hasmeta = 1 ]; then
+
+                # If it was newly created, it will be empty, so delete it.
+                if ! [ "$(ls -A "$bdir")" ]; then rm --dir "$bdir"; fi
+
+                # Inform the user and set 'bdir' to empty again.
+                bdir=
+                echo " ** Build directory should not contain meta-characters"
+                echo " ** (like SPACE, %, \$, !, ;, or parenthesis, among "
+                echo " ** others): they can interrup the build for some software."
+            fi
+        fi
+
+	# If everything is still fine so far, see if we're able to
+	# manipulate file permissions in the directory's filesystem and if
+	# so, see if there is atleast 5GB free space.
 	if ! [ x"$bdir" = x ]; then
-            if ! $(check_permission $bdir); then
+            if ! $(IFS='"' check_permission "$bdir"); then
                 # Unable to handle permissions well
                 bdir=
                 echo " ** File permissions can't be modified in this directory"
@@ -804,7 +881,7 @@ EOF
                 # Able to handle permissions, now check for 5GB free space
                 # in the given partition (note that the number is in units
                 # of 1024 bytes). If this is not the case, print a warning.
-                if $(free_space_warning 5000000 $bdir); then
+                if $(free_space_warning 5000000 "$bdir"); then
                     echo " !! LESS THAN 5GB FREE SPACE IN: $bdir"
                     echo " !! We recommend choosing another partition."
                     echo " !! Build will continue in 5 seconds..."
@@ -817,7 +894,7 @@ EOF
         # reset `build_dir' to blank, so it continues asking for another
         # directory and let the user know that they must select a new
         # directory.
-        if [ x$bdir = x ]; then
+        if [ x"$bdir" = x ]; then
             build_dir=
             echo " ** Please select another directory."
             echo ""
@@ -834,9 +911,9 @@ fi
 # Input directory
 # ---------------
 if [ x"$input_dir" = x ]; then
-    indir=$optionaldir
+    indir="$optionaldir"
 else
-    indir=$input_dir
+    indir="$input_dir"
 fi
 noninteractive_sleep=2
 if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
@@ -878,7 +955,7 @@ EOF
 
     # In case an input-directory is given, write it in 'indir'.
     if [ x$inindir != x ]; then
-        indir=$(absolute_dir $inindir)
+        indir="$(absolute_dir "$inindir")"
         echo " -- Using '$indir'"
     fi
 fi
@@ -922,7 +999,7 @@ EOF
 
     # If given, write the software directory.
     if [ x"$tmpddir" != x ]; then
-        ddir=$(absolute_dir $tmpddir)
+        ddir="$(absolute_dir "$tmpddir")"
         echo " -- Using '$ddir'"
     fi
 fi
@@ -946,11 +1023,18 @@ if [ $rewritepconfig = yes ]; then
         -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
         $pconf.in >> $pconf
 else
-    # Read the values from existing configuration file.
-    inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)
-
-    # Read the software directory.
-    ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)
+    # Read the values from existing configuration file. Note that the build
+    # directory may have space characters. Even though we currently check
+    # against it, we hope to be able to remove this condition in the
+    # future.
+    inbdir=$(awk '$1=="BDIR" { for(i=3; i<NF; i++) \
+                               printf "%s ", $i; \
+                               printf "%s", $NF }' $pconf)
+
+    # Read the software directory (same as 'inbdir' above about space).
+    ddir=$(awk '$1=="DEPENDENCIES-DIR" { for(i=3; i<NF; i++) \
+                                         printf "%s ", $i; \
+                                         printf "%s", $NF}' $pconf)
 
     # The downloader command may contain multiple elements, so we'll just
     # change the (in memory) first and second tokens to empty space and
@@ -968,9 +1052,9 @@ else
     # Make sure `bdir' is an absolute path and it exists.
     berr=0
     ierr=0
-    bdir=$(absolute_dir $inbdir)
+    bdir="$(absolute_dir "$inbdir")"
 
-    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
+    if ! [ -d "$bdir"  ]; then if ! mkdir "$bdir"; then berr=1; err=1; fi; fi
     if [ $err = 1 ]; then
         cat <<EOF
 
@@ -1013,10 +1097,10 @@ fi
 # (without the user noticing), in the end of this script we make a file and
 # we'll delete it here (at the start). Therefore if the script crashed in
 # the middle that file won't exist.
-sdir=$bdir/software
-finaltarget=$sdir/configuration-done.txt
-if ! [ -d $sdir ];  then mkdir $sdir; fi
-rm -f $finaltarget
+sdir="$bdir"/software
+finaltarget="$sdir"/configuration-done.txt
+if ! [ -d "$sdir" ];  then mkdir "$sdir"; fi
+rm -f "$finaltarget"
 
 
 
@@ -1030,56 +1114,56 @@ rm -f $finaltarget
 # analysis Makefiles (thus making them hard to read), we are just building
 # them here
 # Software tarballs
-tardir=$sdir/tarballs
-if ! [ -d $tardir ];  then mkdir $tardir; fi
+tardir="$sdir"/tarballs
+if ! [ -d "$tardir" ];  then mkdir "$tardir"; fi
 
 # Installed software
-instdir=$sdir/installed
-if ! [ -d $instdir ]; then mkdir $instdir; fi
+instdir="$sdir"/installed
+if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi
 
 # To record software versions and citation.
-verdir=$instdir/version-info
-if ! [ -d $verdir ]; then mkdir $verdir; fi
+verdir="$instdir"/version-info
+if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi
 
 # Program and library versions and citation.
-ibidir=$verdir/proglib
-if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+ibidir="$verdir"/proglib
+if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
 
 # Python module versions and citation.
-ipydir=$verdir/python
-if ! [ -d $ipydir ]; then mkdir $ipydir; fi
+ipydir="$verdir"/python
+if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
 
 # Used software BibTeX entries.
-ictdir=$verdir/cite
-if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+ictdir="$verdir"/cite
+if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
 
 # TeXLive versions.
-itidir=$verdir/tex
-if ! [ -d $itidir ]; then mkdir $itidir; fi
+itidir="$verdir"/tex
+if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
 
 # Top-level LaTeX.
-texdir=$bdir/tex
-if ! [ -d $texdir ]; then mkdir $texdir; fi
+texdir="$bdir"/tex
+if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi
 
 # LaTeX macros.
-mtexdir=$texdir/macros
-if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
+mtexdir="$texdir"/macros
+if ! [ -d "$mtexdir" ]; then mkdir "$mtexdir"; fi
 
 
 # TeX build directory. If built in a group scenario, the TeX build
 # directory must be separate for each member (so they can work on their
 # relevant parts of the paper without conflicting with each other).
 if [ "x$reproducible_paper_group_name" = x ]; then
-    texbdir=$texdir/build
+    texbdir="$texdir"/build
 else
     user=$(whoami)
-    texbdir=$texdir/build-$user
+    texbdir="$texdir"/build-$user
 fi
-if ! [ -d $texbdir ]; then mkdir $texbdir; fi
+if ! [ -d "$texbdir" ]; then mkdir "$texbdir"; fi
 
 # TiKZ (for building figures within LaTeX).
-tikzdir=$texbdir/tikz
-if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
+tikzdir="$texbdir"/tikz
+if ! [ -d "$tikzdir" ]; then mkdir "$tikzdir"; fi
 
 # If 'tex/build' and 'tex/tikz' aren't symbolic links, then we are in the
 # tarball (not the Git repository), so we'll give them another name and let
@@ -1120,14 +1204,14 @@ fi
 # safe, we are deleting all the links on each re-configure of the project.
 rm -f .build .local
 
-ln -s $bdir .build
-ln -s $instdir .local
-ln -s $texdir tex/build
-ln -s $tikzdir tex/tikz
+ln -s "$bdir" .build
+ln -s "$instdir" .local
+ln -s "$texdir" tex/build
+ln -s "$tikzdir" tex/tikz
 
 # --------- Delete for no Gnuastro ---------
 rm -f .gnuastro
-ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
+ln -s "$topdir"/reproduce/analysis/config/gnuastro .gnuastro
 # ------------------------------------------
 
 
@@ -1143,8 +1227,8 @@ ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
 # project names). Maybe later, we can use something like `mktemp' to add
 # random characters to this name and make it unique to every run (even for
 # a single user).
-tmpblddir=$sdir/build-tmp
-rm -rf $tmpblddir/* $tmpblddir  # If its a link, we need to empty its
+tmpblddir="$sdir"/build-tmp
+rm -rf "$tmpblddir"/* "$tmpblddir"  # If its a link, we need to empty its
                                 # contents first, then itself.
 
 # Set the top-level shared memory location.
@@ -1156,12 +1240,12 @@ fi
 # there (in RAM), build a temporary directory for this project.
 needed_space=2000000
 if [ x"$shmdir" != x ]; then
-    available_space=$(df $shmdir | awk 'NR==2{print $4}')
+    available_space=$(df "$shmdir" | awk 'NR==2{print $4}')
     if [ $available_space -gt $needed_space ]; then
         dirname=$(pwd | sed -e's/\// /g' \
                       | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
-        tbshmdir=$shmdir/"$dirname"-$(whoami)
-        if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
+        tbshmdir="$shmdir"/"$dirname"-$(whoami)
+        if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
     fi
 else
     tbshmdir=""
@@ -1170,8 +1254,8 @@ fi
 # If a shared memory directory was created set `build-tmp' to be a
 # symbolic link to it. Otherwise, just build the temporary build
 # directory under the project build directory.
-if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
-else                        ln -s $tbshmdir $tmpblddir;
+if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir";
+else                        ln -s "$tbshmdir" "$tmpblddir";
 fi
 
 
@@ -1540,6 +1624,24 @@ fi
 
 
 
+# Report machine architecture
+# ---------------------------
+#
+# Report hardware
+hwparam="$mtexdir/hardware-parameters.tex"
+
+# Add the text to the ${hwparam} file. Since harware class might include
+# underscore, it must be replaced with '\_', otherwise pdftex would
+# complain and break the build process when doing ./project make.
+hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
+.local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" > $hwparam
+.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam
+.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam
+
+
+
+
+
 # Clean the temporary build directory
 # ---------------------------------
 #
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 9188fc9..a18966f 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -30,32 +30,32 @@ set -e
 
 
 
-# Input arguments.
-bdir=$1
-ddir=$2
-downloader="$3"
-user_backup_urls="$4"
+# Input arguments (the 'IFS's are to allow space in the name).
+IFS='"' bdir="$1"
+IFS='"' ddir="$2"
+IFS='"' downloader="$3"
+IFS='"' user_backup_urls="$4"
 
 
 
 
 
 # Basic directories/files
-topdir=$(pwd)
-sdir=$bdir/software
-tardir=$sdir/tarballs
-instdir=$sdir/installed
-tmpblddir=$sdir/build-tmp
+topdir="$(pwd)"
+sdir="$bdir"/software
+tardir="$sdir"/tarballs
+instdir="$sdir"/installed
+tmpblddir="$sdir"/build-tmp
 confdir=reproduce/software/config
-ibidir=$instdir/version-info/proglib
+ibidir="$instdir"/version-info/proglib
 downloadwrapper=reproduce/analysis/bash/download-multi-try
 
 # Derived directories
-bindir=$instdir/bin
-urlfile=$confdir/urls.conf
-versionsfile=$confdir/versions.conf
-checksumsfile=$confdir/checksums.conf
-backupfile=$confdir/servers-backup.conf
+bindir="$instdir"/bin
+urlfile="$confdir"/urls.conf
+versionsfile="$confdir"/versions.conf
+checksumsfile="$confdir"/checksums.conf
+backupfile="$confdir"/servers-backup.conf
 
 
 
@@ -87,21 +87,21 @@ done
 # Download the necessary tarball.
 download_tarball() {
   # Basic definitions
-  maneagetar=$tardir/$tarball
+  maneagetar="$tardir"/"$tarball"
 
   # See if the tarball already exists in Maneage.
   if [ -f "$maneagetar" ]; then
     just_a_place_holder=1
   else
-    ucname=$tardir/$tarball.unchecked
+    ucname="$tardir"/"$tarball.unchecked"
 
     # If the URL is empty, use the top backup server
     if [ x$w = x ]; then
         bservers="$backupservers"
-        tarballurl=$topbackupserver/$tarball
+        tarballurl="$topbackupserver"/"$tarball"
     else
         bservers="$backupservers_all"
-        tarballurl=$url/$tarball
+        tarballurl="$url"/"$tarball"
     fi
 
     # See if it is in the input-software directory, if so, make a link, if
@@ -111,19 +111,19 @@ download_tarball() {
     # link and link to an actual file.
     if [ -f "$ddir/$tarball" ]; then
       if type realpath > /dev/null 2> /dev/null; then
-        ln -sf "$(realpath $ddir/$tarball)" "$ucname"
+        ln -sf "$(realpath "$ddir/$tarball")" "$ucname"
       else
-        cp $ddir/$tarball $ucname
+        cp "$ddir/$tarball" "$ucname"
       fi
     else
-      $downloadwrapper "$downloader" nolock $tarballurl $ucname \
+      $downloadwrapper "$downloader" nolock $tarballurl "$ucname" \
                        "$bservers"
     fi
 
     # Make sure this is the correct tarball.
     if type sha512sum > /dev/null 2> /dev/null; then
       checksum=$(sha512sum "$ucname" | awk '{print $1}')
-      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile)
+      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile")
       if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
       else
         echo "ERROR: Non-matching checksum: $tarball"
@@ -137,9 +137,9 @@ download_tarball() {
 
   # If the tarball is newer than the (possibly existing) program (the version
   # has changed), then delete the program.
-  if [ -f $ibidir/$progname ]; then
-      if [ $maneagetar -nt $ibidir/$progname ]; then
-          rm $ibidir/$progname
+  if [ -f "$ibidir/$progname" ]; then
+      if [ "$maneagetar" -nt "$ibidir/$progname" ]; then
+          rm "$ibidir/$progname"
       fi
   fi
 }
@@ -151,39 +151,39 @@ download_tarball() {
 # Build the program from the tarball. This function takes one argument
 # which is the configure-time options.
 build_program() {
-  if ! [ -f $ibidir/$progname ]; then
+  if ! [ -f "$ibidir/$progname" ]; then
 
     # Options
     configoptions=$1
 
     # Go into the temporary building directory.
-    cd $tmpblddir
+    cd "$tmpblddir"
     unpackdir="$progname"-"$version"
 
     # Some implementations of 'tar' don't recognize Lzip, so we need to
     # manually call Lzip first, then call tar afterwards.
-    csuffix=$(echo $tarball | sed -e's/\./ /g' | awk '{print $NF}')
-    rm -rf $unpackdir
+    csuffix=$(echo "$tarball" | sed -e's/\./ /g' | awk '{print $NF}')
+    rm -rf "$unpackdir"
     if [ x$csuffix = xlz ]; then
       intarrm=1
-      intar=$(echo $tarball | sed -e's/.lz//')
-      lzip -c -d $tardir/$tarball > $intar
+      intar=$(echo "$tarball" | sed -e's/.lz//')
+      lzip -c -d "$tardir/$tarball" > $intar
     else
       intarrm=0
-      intar=$tardir/$tarball
+      intar="$tardir"/"$tarball"
     fi
 
     # Unpack the tarball and go into it.
-    tar xf $intar
-    if [ x$intarrm = x1 ]; then rm $intar; fi
-    cd $unpackdir
+    tar xf "$intar"
+    if [ x$intarrm = x1 ]; then rm "$intar"; fi
+    cd "$unpackdir"
 
     # build the project, either with Make and either without it.
     if [ x$progname = xlzip ]; then
-        ./configure --build --check --installdir=$instdir/bin $configoptions
+        ./configure --build --check --installdir="$instdir/bin" $configoptions
     else
         # All others accept the configure script.
-        ./configure --prefix=$instdir $configoptions
+        ./configure --prefix="$instdir" $configoptions
 
         # To build GNU Make, we don't want to assume the existance of a
         # Make program, so we use its 'build.sh' script and its own built
@@ -198,9 +198,9 @@ build_program() {
     fi
 
     # Clean up the source directory
-    cd $topdir
-    rm -rf $tmpblddir/$unpackdir
-    echo "$progname_tex $version" > $ibidir/$progname
+    cd "$topdir"
+    rm -rf "$tmpblddir/$unpackdir"
+    echo "$progname_tex $version" > "$ibidir/$progname"
   fi
 }
 
@@ -219,7 +219,7 @@ build_program() {
 progname="lzip"
 progname_tex="Lzip"
 url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
-version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
+version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile")
 tarball=$progname-$version.tar
 download_tarball
 build_program