Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

3 files changed, 6 insertions, 60 deletions

diff --git a/reproduce/software/patches/README.md b/reproduce/software/patches/README.md
new file mode 100644
index 0000000..804d7ec
--- /dev/null
+++ b/reproduce/software/patches/README.md
@@ -0,0 +1,6 @@
+Patches to apply to software source
+===================================
+
+This directory is for keeping patches that may be necessary for some
+versions of some software. So it may be empty in some instances (when no
+software in that commit needs a patch).
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
deleted file mode 100644
index 94dcab5..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
+++ /dev/null
@@ -1,37 +0,0 @@
----
- mpi/libmpiwrap.c |   12 +++++++++++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=10
- and hacked further by Boud Roukema 2020-05-10.
---- a/mpi/libmpiwrap.c
-+++ b/mpi/libmpiwrap.c
-@@ -278,8 +278,12 @@ static void showTy ( FILE* f, MPI_Dataty
-    else if (ty == MPI_LONG_INT)       fprintf(f,"LONG_INT");
-    else if (ty == MPI_SHORT_INT)      fprintf(f,"SHORT_INT");
-    else if (ty == MPI_2INT)           fprintf(f,"2INT");
-+#  if defined(MPI_UB_ENABLED_IN_MPI1)
-    else if (ty == MPI_UB)             fprintf(f,"UB");
-+#  endif
-+#  if defined(MPI_LB_ENABLED_IN_MPI1)
-    else if (ty == MPI_LB)             fprintf(f,"LB");
-+#  endif
- #  if defined(MPI_WCHAR)
-    else if (ty == MPI_WCHAR)          fprintf(f,"WCHAR");
- #  endif
-@@ -733,8 +737,14 @@ void walk_type ( void(*f)(void*,long), c
-          f(base + offsetof(Ty,loc), sizeof(int));
-          return;
-       }
--      if (ty == MPI_LB || ty == MPI_UB)
-+#if defined(MPI_LB_ENABLED_IN_MPI1)
-+      if (ty == MPI_LB)
-+         return; /* have zero size, so nothing needs to be done */
-+#endif
-+#if defined(MPI_UB_ENABLED_IN_MPI1)
-+      if (ty == MPI_UB)
-          return; /* have zero size, so nothing needs to be done */
-+#endif
-       goto unhandled;
-       /*NOTREACHED*/
-    }
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
deleted file mode 100644
index 12b50a2..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Index: valgrind-3.15.0/mpi/Makefile.am
-===================================================================
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=22
---- valgrind-3.15.0.orig/mpi/Makefile.am
-+++ valgrind-3.15.0/mpi/Makefile.am
-@@ -42,14 +42,14 @@ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CFLAGS   = \
- 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_PRI) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
- endif
- if BUILD_MPIWRAP_SEC
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_SOURCES  = libmpiwrap.c
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CFLAGS   = \
- 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_SEC) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
- endif
- 
- #----------------------------------------------------------------------------