Imported recent work on Maneage, minor conflicts fixed

A few minor conflicts occurred and were fixed.

7 files changed, 30 insertions, 31 deletions

diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index e4f2ccd..cf5bfa4 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -24,9 +24,10 @@
 # Download input data
 # --------------------
 #
-# The input dataset properties are defined in `$(pconfdir)/INPUTS.mk'. For
-# this template we only have one dataset to enable easy processing, so all
-# the extra checks in this rule may seem redundant.
+# The input dataset properties are defined in
+# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
+# enable easy processing, so all the extra checks in this rule may seem
+# redundant.
 #
 # In a real project, you will need more than one dataset. In that case,
 # just add them to the target list and add an `elif' statement to define it
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index a4acff7..ce4e488 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -141,6 +141,12 @@ export SHELL := $(installdir)/bin/bash
 export CPPFLAGS := -I$(installdir)/include
 export LD_LIBRARY_PATH := $(installdir)/lib
 
+# Until we build our own C library, without this, the project's GCC won't
+# be able to compile anything if the host C library isn't in a standard
+# place: in particular Debian-based operatings sytems. On other systems, it
+# will be empty.
+export CPATH := $(SYS_CPATH)
+
 # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
@@ -151,9 +157,9 @@ export DYLD_LIBRARY_PATH :=
 # remote-shell accesss through this environment variable.
 export OMPI_MCA_plm_rsh_agent=/bin/false
 
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
 export PROJECT_STATUS := make
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 
 
 
@@ -242,7 +248,7 @@ distclean: clean
         # `rm', not our own.
 	$$sys_rm -rf $(BDIR)
 	$$sys_rm -f Makefile .gnuastro .local .build
-	$$sys_rm -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf
+	$$sys_rm -f $(pconfdir)/LOCAL.conf $(gconfdir)/gnuastro-local.conf
 
 
 
@@ -299,10 +305,11 @@ $(packagecontents): paper.pdf | $(texdir)
         # directories (when building in a group structure, there will be
         # `build-user1', `build-user2' and etc), are just temporary LaTeX
         # build files and don't have any relevant/hand-written files in
-        # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have
-        # this machine's local settings and are irrelevant for anyone else.
+        # them. 2) The `LOCAL.conf' and `gnuastro-local.conf' files just
+        # have this machine's local settings and are irrelevant for anyone
+        # else.
 	rm -rf $$dir/tex/build/build*
-	rm $$dir/reproduce/software/config/installation/LOCAL.mk
+	rm $$dir/reproduce/software/config/installation/LOCAL.conf
 	rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf
 
         # When submitting to places like arXiv, they will just run LaTeX
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index af6bdc5..67db364 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -38,7 +38,7 @@
 #
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can remove the value of `pdf-build-final' in
-# `reproduce/analysis/config/pdf-build.mk'.
+# `reproduce/analysis/config/pdf-build.conf'.
 $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
         # If no PDF is requested, or if LaTeX isn't available, don't
@@ -62,7 +62,7 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	    echo "can check by running './.local/bin/latex --version'), _AND_"
 	    echo "make sure that the 'pdf-build-final' variable has a value."
 	    echo "'pdf-build-final' is defined in: "
-	    echo     "'reproduce/analysis/config/pdf-build.mk'."
+	    echo     "'reproduce/analysis/config/pdf-build.conf'."
 	    echo
 	    echo "If you don't have LaTeX within the project, please re-run"
 	    echo "'./project configure -e' when you have internet access."
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index 1f0613c..36f25e7 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -19,7 +19,9 @@
 # Final-target
 #
 # Without this file, `./project make' won't work.
-$(BDIR)/software/preparation-done.mk:
+prepare-dep = $(subst prepare, ,$(makesrc))
+$(BDIR)/software/preparation-done.mk: \
+                $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
 
         # If you need to add preparations define targets above to do the
         # preparations, then set the value below to `yes'. Recall that just
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 000c1fd..30d537a 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -21,7 +21,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.mk
+include reproduce/software/config/installation/LOCAL.conf
 
 
 
@@ -50,7 +50,7 @@ include reproduce/software/config/installation/LOCAL.mk
 #
 # Controlling this requires two variables that are available at this stage:
 #
-#   - `GROUP-NAME': from `LOCAL.mk' (which was built by `./project configure').
+#   - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
 #   - `reproducible_paper_group_name': value to the `--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
@@ -63,7 +63,7 @@ include reproduce/software/config/installation/LOCAL.mk
 #
 # If you are just interested in the processing and don't want to build the
 # PDF, you can skip the creatation of the final PDF by removing the value
-# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.mk'.
+# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
 all: paper.pdf
 else
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index 5ce120d..1778c6b 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -25,7 +25,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.mk
+include reproduce/software/config/installation/LOCAL.conf
 
 
 
@@ -37,19 +37,7 @@ include reproduce/software/config/installation/LOCAL.mk
 # See `top-make.mk' for complete explanation.
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
 all: $(BDIR)/software/preparation-done.mk
-	@echo "";
-	echo "----------------"
-	echo "Project preparation has been completed without any errors."
-	echo ""
-	echo "Please run the following command to start building the project."
-	echo "(Replace '8' with the number of CPU threads on your system)"
-	echo ""
-	if [ "x$(GROUP-NAME)" = x ]; then \
-	  echo "   $$ ./project make"; \
-	else \
-	  echo "   $$ ./project make --group=$(GROUP-NAME) -j8"; \
-	fi
-	echo ""
+	@echo "Project preparation is complete.";
 else
 all:
 	@if [ "x$(GROUP-NAME)" = x ]; then \
@@ -59,6 +47,7 @@ all:
 	  echo "Project is configured for groups, please run"; \
 	  echo "   $$ ./project prepare --group=$(GROUP-NAME) -j8"; \
 	fi
+	exit 1
 endif
 
 
@@ -87,5 +76,5 @@ makesrc = initialize \
 #
 # See `top-make.mk' for complete explanation.
 project-phase = prepare
-include reproduce/analysis/config/*.mk
+include reproduce/analysis/config/*.conf
 include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index a04bce4..f0bcf10 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -33,7 +33,7 @@ verify-print-tips = \
   echo "If you are still developing your project, you can disable"; \
   echo "verification by removing the value of the variable in the"; \
   echo "following file (from the top project source directory):"; \
-  echo "    reproduce/analysis/config/verify-outputs.mk"; \
+  echo "    reproduce/analysis/config/verify-outputs.conf"; \
   echo; \
   echo "If this is the final version of the file, you can just copy"; \
   echo "and paste the calculated checksum (above) for the file in"; \