From b7bf93cad5b77c754ad3091f83080b0007e02b23 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 28 Sep 2016 20:13:05 -0500
Subject: [PATCH 01/44] Added a C++ version of dirname() which handles the
 maybe-modified/maybe-allocated/maybe-static arg and result strings for the
 caller.

---
 src/libext/filesystem.hpp | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/src/libext/filesystem.hpp b/src/libext/filesystem.hpp
index 1fd46e4f..4c77c953 100644
--- a/src/libext/filesystem.hpp
+++ b/src/libext/filesystem.hpp
@@ -24,6 +24,17 @@
 
 #include <sys/stat.h>
 #include <sys/types.h> // for dev_t, ino_t
+// Don't know where the name "libgen" comes from, but this is where POSIX says dirname() and basename() are declared.
+/// There are two basename()s.  GNU basename, from string.h, and POSIX basename() from libgen.h.
+/// See notes here: https://linux.die.net/man/3/dirname
+/// Of course they behave slightly differently: GNU version returns an empty string if the path has a trailing slash, and doesn't modify it's argument.
+/// To complicate matters further, the glibc version of the POSIX function versions do modify their args.
+/// And at least NetBSD behaves similarly.  So, include the POSIX versions and we'll try to clean this mess up below.
+#include <libgen.h>
+
+/// @note Because we included libgen.h above, we shouldn't get the GNU version from this #include of string.h.
+#include <string.h>
+#include <string>
 
 #include "integer.hpp"
 
@@ -71,4 +82,25 @@ inline bool is_same_file(int fd1, int fd2)
 	}
 }
 
+
+/**
+ * A more usable and portable replacement for GNU and POSIX dirname().
+ *
+ * @param path
+ * @return
+ */
+inline std::string dirname(const std::string &path)
+{
+	// Get a copy of the path string which dirname() can modify all it wants.
+	char * modifiable_path = strdup(path.c_str());
+
+	// Copy the output of dirname into a std:string.  We don't ever free the string dirname() returns
+	// because it's either a static buffer, or it's a pointer to modifiable_path.  The latter we'll free below.
+	std::string retval(dirname(modifiable_path));
+
+	free(modifiable_path);
+
+	return retval;
+}
+
 #endif /* SRC_LIBEXT_FILESYSTEM_HPP_ */

From 147ee36c2473e41d18fe0505ec63f914ac577751 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 29 Sep 2016 19:19:51 -0500
Subject: [PATCH 02/44] Interim.

---
 src/ArgParse.cpp          | 15 ++++++++-------
 src/libext/filesystem.hpp | 11 ++++++++---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/ArgParse.cpp b/src/ArgParse.cpp
index 430a277e..c3373259 100644
--- a/src/ArgParse.cpp
+++ b/src/ArgParse.cpp
@@ -57,7 +57,7 @@
 #include <fcntl.h>
 #include <unistd.h> // for GetUserHomeDir()-->getuid().
 #include <sys/stat.h>
-#include <libgen.h>   // Don't know where the name "libgen" comes from, but this is where POSIX says dirname() and basename() are declared.
+//#include <libgen.h>   // Don't know where the name "libgen" comes from, but this is where POSIX says dirname() and basename() are declared.
 
 #include <libext/string.hpp>
 #include <libext/filesystem.hpp>
@@ -752,16 +752,17 @@ std::string ArgParse::GetProjectRCFilename() const
 	char *original_cwd = getcwd(NULL, 0);
 #endif
 
+
 	LOG(INFO) << "cwd = \'" << original_cwd << "\'";
 
-	char *current_cwd = original_cwd;
-	while((current_cwd != nullptr) && (current_cwd[0] != '.'))
+	std::string current_cwd(original_cwd == nullptr ? "" : original_cwd);
+	while(!current_cwd.empty() && current_cwd[0] != '.')
 	{
 		// If we were able to get a file descriptor to $HOME above...
 		if(home_fd != -1)
 		{
 			// ...check if this dir is the user's $HOME dir.
-			int cwd_fd = open(current_cwd, O_RDONLY);
+			int cwd_fd = open(current_cwd.c_str(), O_RDONLY);
 			if(cwd_fd != -1)
 			{
 				/// @todo Should probably check for is-a-dir here.
@@ -777,7 +778,7 @@ std::string ArgParse::GetProjectRCFilename() const
 		}
 
 		// Try to open the config file.
-		auto test_rc_filename = std::string(current_cwd);
+		auto test_rc_filename = current_cwd;
 		if(*test_rc_filename.rbegin() != '/')
 		{
 			test_rc_filename += "/";
@@ -797,14 +798,14 @@ std::string ArgParse::GetProjectRCFilename() const
 		/// @note GRVS - get_current_dir_name() under Cygwin will currently return a DOS path if this is started
 		///              under the Eclipse gdb.  This mostly doesn't cause problems, except for terminating the loop.
 		///              The clause below after the || handles this.
-		if((std::strlen(current_cwd) == 1) || (std::strlen(current_cwd) <= 4 && current_cwd[1] == ':'))
+		if((current_cwd.length() == 1) || (current_cwd.length() <= 4 && current_cwd[1] == ':'))
 		{
 			// We've hit the root and didn't find a config file.
 			break;
 		}
 
 		// Go up one directory.
-		current_cwd = dirname(current_cwd);
+		current_cwd = portable::dirname(current_cwd);
 	}
 
 	// Free the cwd string.
diff --git a/src/libext/filesystem.hpp b/src/libext/filesystem.hpp
index 4c77c953..5af02621 100644
--- a/src/libext/filesystem.hpp
+++ b/src/libext/filesystem.hpp
@@ -82,12 +82,15 @@ inline bool is_same_file(int fd1, int fd2)
 	}
 }
 
+namespace portable
+{
 
 /**
- * A more usable and portable replacement for GNU and POSIX dirname().
+ * A more usable and portable replacement for glibc and POSIX dirname().
  *
- * @param path
- * @return
+ * @param path  const ref to a path string.  Guaranteed to not be modified in any way by the function call.
+ * @return  A std::string representing the path to return the directory of.  Guaranteed to be a normal std::string with which you may do
+ *          whatever you can do with any other std::string.
  */
 inline std::string dirname(const std::string &path)
 {
@@ -103,4 +106,6 @@ inline std::string dirname(const std::string &path)
 	return retval;
 }
 
+}
+
 #endif /* SRC_LIBEXT_FILESYSTEM_HPP_ */

From fc2c0f729dee3db0295878d4d07b49fcd86a02f8 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 29 Sep 2016 20:05:09 -0500
Subject: [PATCH 03/44] Fixed infinite recursion.

---
 src/libext/filesystem.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/libext/filesystem.hpp b/src/libext/filesystem.hpp
index 5af02621..6428d410 100644
--- a/src/libext/filesystem.hpp
+++ b/src/libext/filesystem.hpp
@@ -99,7 +99,7 @@ inline std::string dirname(const std::string &path)
 
 	// Copy the output of dirname into a std:string.  We don't ever free the string dirname() returns
 	// because it's either a static buffer, or it's a pointer to modifiable_path.  The latter we'll free below.
-	std::string retval(dirname(modifiable_path));
+	std::string retval(::dirname(modifiable_path));
 
 	free(modifiable_path);
 

From 5ee7e35fc8e3e87fe30d317e7f95decc22309380 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 29 Sep 2016 20:14:10 -0500
Subject: [PATCH 04/44] Add <cstdlib> so we have a prototype for free().

---
 src/libext/filesystem.hpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/libext/filesystem.hpp b/src/libext/filesystem.hpp
index 6428d410..71b4a9e7 100644
--- a/src/libext/filesystem.hpp
+++ b/src/libext/filesystem.hpp
@@ -34,6 +34,7 @@
 
 /// @note Because we included libgen.h above, we shouldn't get the GNU version from this #include of string.h.
 #include <string.h>
+#include <cstdlib>   // For free().
 #include <string>
 
 #include "integer.hpp"

From 8584819fe0c63ce72dc303c5efe80e7f5fe36b98 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 29 Sep 2016 20:50:31 -0500
Subject: [PATCH 05/44] Updated NEWS.md for bug/ISSUE96-dirname.

---
 NEWS.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 1491588d..fe0ec5c9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -30,7 +30,8 @@
 ### Fixed
 - Cygwin now requires AC_USE_SYSTEM_EXTENSIONS for access to get_current_dir_name().  Resolves #76.
 - Resolved issue with highlights on wrapped lines sometimes extending the full width of the terminal.  Resolves #80.
-- Resolved issue where matches spanning an eol (e.g. 'a\s+b' matching 'a\nb') would cause the program to throw an exception and terminate.  Resolves #92. 
+- Resolved issue where matches spanning an eol (e.g. 'a\s+b' matching 'a\nb') would cause the program to throw an exception and terminate.  Resolves #92.
+- Resolved segfaults on some systems due to dirname() modifying its parameter.  Resolves #96.
 
 
 ## [0.2.2] - 2016-04-09

From 038e498679dcce932469089ff794176e44d7024c Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Fri, 30 Sep 2016 08:40:33 -0500
Subject: [PATCH 06/44] Portability fix: test == to test =.

---
 configure.ac | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/configure.ac b/configure.ac
index 042f3881..d23c5bab 100644
--- a/configure.ac
+++ b/configure.ac
@@ -149,7 +149,7 @@ AC_PROG_EGREP
 AC_PROG_FGREP
 AC_PROG_AWK
 AC_PROG_LN_S
-AS_IF([test "$LN_S" == 'ln -s'],
+AS_IF([test "$LN_S" = 'ln -s'],
 	[AC_SUBST([TEST_LN_S], [$LN_S])],
 	[AC_SUBST([TEST_LN_S], [:])
 	AC_MSG_WARN([couldn't find a real 'ln -s', will not be able to run all tests])])
@@ -345,7 +345,7 @@ AM_COND_IF([BUILD_X86_64_ISA_EXTENSIONS],
 # optionally use some pthreads functionality, e.g. naming threads for diagnostic, logging, and other purposes.
 # Macro docs: http://www.gnu.org/software/autoconf-archive/ax_pthread.html#ax_pthread
 AX_PTHREAD
-AS_IF([test "x$ax_pthread_ok" == xyes],
+AS_IF([test "x$ax_pthread_ok" = xyes],
 	[
 		AC_MSG_NOTICE([found pthreads])
 		AC_MSG_CHECKING([if the C++11 underlying thread implementation is pthreads])
@@ -353,8 +353,7 @@ AS_IF([test "x$ax_pthread_ok" == xyes],
         [AC_LANG_PROGRAM([
         					#include <type_traits>
         					#include <thread>
-        					#include <pthread.h>
-        					
+        					#include <pthread.h> 					
         				],
                          [
                          	static_assert(std::is_same<std::thread::native_handle_type, pthread_t>::value, "C++11 underlying thread implementation is not pthreads");

From 75a14441281732427512887eb849068cd54c3459 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sat, 1 Oct 2016 20:51:24 -0500
Subject: [PATCH 07/44] Updated some M4 macros to GNU Autoconf Archive version
 2016.09.16.

---
 m4/ax_count_cpus.m4            | 113 ++++---
 m4/ax_cxx_compile_stdcxx.m4    |  14 +-
 m4/ax_cxx_compile_stdcxx_11.m4 |   8 +-
 m4/ax_gcc_builtin.m4           |   4 +-
 m4/ax_prog_doxygen.m4          |   5 +-
 m4/ax_pthread.m4               | 550 ++++++++++++++++-----------------
 6 files changed, 369 insertions(+), 325 deletions(-)

diff --git a/m4/ax_count_cpus.m4 b/m4/ax_count_cpus.m4
index eeecccf5..0922e702 100644
--- a/m4/ax_count_cpus.m4
+++ b/m4/ax_count_cpus.m4
@@ -4,18 +4,21 @@
 #
 # SYNOPSIS
 #
-#   AX_COUNT_CPUS
+#   AX_COUNT_CPUS([ACTION-IF-DETECTED],[ACTION-IF-NOT-DETECTED])
 #
 # DESCRIPTION
 #
-#   Attempt to count the number of processors present on the machine. If the
-#   detection fails, then a value of 1 is assumed.
+#   Attempt to count the number of logical processor cores (including
+#   virtual and HT cores) currently available to use on the machine and
+#   place detected value in CPU_COUNT variable.
 #
-#   The value is placed in the CPU_COUNT variable.
+#   On successful detection, ACTION-IF-DETECTED is executed if present. If
+#   the detection fails, then ACTION-IF-NOT-DETECTED is triggered. The
+#   default ACTION-IF-NOT-DETECTED is to set CPU_COUNT to 1.
 #
 # LICENSE
 #
-#   Copyright (c) 2014 Karlson2k (Evgeny Grin) <k2k@narod.ru>
+#   Copyright (c) 2014,2016 Karlson2k (Evgeny Grin) <k2k@narod.ru>
 #   Copyright (c) 2012 Brian Aker <brian@tangent.org>
 #   Copyright (c) 2008 Michael Paul Bailey <jinxidoru@byu.net>
 #   Copyright (c) 2008 Christophe Tournayre <turn3r@users.sourceforge.net>
@@ -25,42 +28,74 @@
 #   and this notice are preserved. This file is offered as-is, without any
 #   warranty.
 
-#serial 11
+#serial 21
 
-  AC_DEFUN([AX_COUNT_CPUS],[
-      AC_REQUIRE([AC_CANONICAL_HOST])
-      AC_REQUIRE([AC_PROG_EGREP])
+  AC_DEFUN([AX_COUNT_CPUS],[dnl
+      AC_REQUIRE([AC_CANONICAL_HOST])dnl
+      AC_REQUIRE([AC_PROG_EGREP])dnl
       AC_MSG_CHECKING([the number of available CPUs])
       CPU_COUNT="0"
 
-      AS_CASE([$host_os],[
-        *darwin*],[
-        AS_IF([test -x /usr/sbin/sysctl],[
-          sysctl_a=`/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.cpu`
-          AS_IF([test sysctl_a],[
-            CPU_COUNT=`/usr/sbin/sysctl -n hw.ncpu`
-            ])
-          ])],[
-        *linux*],[
-        AS_IF([test "x$CPU_COUNT" = "x0" -a -e /proc/cpuinfo],[
-          AS_IF([test "x$CPU_COUNT" = "x0" -a -e /proc/cpuinfo],[
-            CPU_COUNT=`$EGREP -c '^processor' /proc/cpuinfo`
-            ])
-          ])],[
-        *mingw*],[
-        AS_IF([test -n "$NUMBER_OF_PROCESSORS"],[
-          CPU_COUNT="$NUMBER_OF_PROCESSORS"
-          ])],[
-        *cygwin*],[
-        AS_IF([test -n "$NUMBER_OF_PROCESSORS"],[
-          CPU_COUNT="$NUMBER_OF_PROCESSORS"
-          ])
-        ])
+      # Try generic methods
 
-      AS_IF([test "x$CPU_COUNT" = "x0"],[
-        CPU_COUNT="1"
-        AC_MSG_RESULT( [unable to detect (assuming 1)] )
-        ],[
-        AC_MSG_RESULT( $CPU_COUNT )
-        ])
-      ])
+      # 'getconf' is POSIX utility, but '_NPROCESSORS_ONLN' and
+      # 'NPROCESSORS_ONLN' are platform-specific
+      command -v getconf >/dev/null 2>&1 && \
+        CPU_COUNT=`getconf _NPROCESSORS_ONLN 2>/dev/null || getconf NPROCESSORS_ONLN 2>/dev/null` || CPU_COUNT="0"
+      AS_IF([[test "$CPU_COUNT" -gt "0" 2>/dev/null || ! command -v nproc >/dev/null 2>&1]],[[: # empty]],[dnl
+        # 'nproc' is part of GNU Coreutils and is widely available
+        CPU_COUNT=`OMP_NUM_THREADS='' nproc 2>/dev/null` || CPU_COUNT=`nproc 2>/dev/null` || CPU_COUNT="0"
+      ])dnl
+
+      AS_IF([[test "$CPU_COUNT" -gt "0" 2>/dev/null]],[[: # empty]],[dnl
+        # Try platform-specific preferred methods
+        AS_CASE([[$host_os]],dnl
+          [[*linux*]],[[CPU_COUNT=`lscpu -p 2>/dev/null | $EGREP -e '^@<:@0-9@:>@+,' -c` || CPU_COUNT="0"]],dnl
+          [[*darwin*]],[[CPU_COUNT=`sysctl -n hw.logicalcpu 2>/dev/null` || CPU_COUNT="0"]],dnl
+          [[freebsd*]],[[command -v sysctl >/dev/null 2>&1 && CPU_COUNT=`sysctl -n kern.smp.cpus 2>/dev/null` || CPU_COUNT="0"]],dnl
+          [[netbsd*]], [[command -v sysctl >/dev/null 2>&1 && CPU_COUNT=`sysctl -n hw.ncpuonline 2>/dev/null` || CPU_COUNT="0"]],dnl
+          [[solaris*]],[[command -v psrinfo >/dev/null 2>&1 && CPU_COUNT=`psrinfo 2>/dev/null | $EGREP -e '^@<:@0-9@:>@.*on-line' -c 2>/dev/null` || CPU_COUNT="0"]],dnl
+          [[mingw*]],[[CPU_COUNT=`ls -qpU1 /proc/registry/HKEY_LOCAL_MACHINE/HARDWARE/DESCRIPTION/System/CentralProcessor/ 2>/dev/null | $EGREP -e '^@<:@0-9@:>@+/' -c` || CPU_COUNT="0"]],dnl
+          [[msys*]],[[CPU_COUNT=`ls -qpU1 /proc/registry/HKEY_LOCAL_MACHINE/HARDWARE/DESCRIPTION/System/CentralProcessor/ 2>/dev/null | $EGREP -e '^@<:@0-9@:>@+/' -c` || CPU_COUNT="0"]],dnl
+          [[cygwin*]],[[CPU_COUNT=`ls -qpU1 /proc/registry/HKEY_LOCAL_MACHINE/HARDWARE/DESCRIPTION/System/CentralProcessor/ 2>/dev/null | $EGREP -e '^@<:@0-9@:>@+/' -c` || CPU_COUNT="0"]]dnl
+        )dnl
+      ])dnl
+
+      AS_IF([[test "$CPU_COUNT" -gt "0" 2>/dev/null || ! command -v sysctl >/dev/null 2>&1]],[[: # empty]],[dnl
+        # Try less preferred generic method
+        # 'hw.ncpu' exist on many platforms, but not on GNU/Linux
+        CPU_COUNT=`sysctl -n hw.ncpu 2>/dev/null` || CPU_COUNT="0"
+      ])dnl
+
+      AS_IF([[test "$CPU_COUNT" -gt "0" 2>/dev/null]],[[: # empty]],[dnl
+      # Try platform-specific fallback methods
+      # They can be less accurate and slower then preferred methods
+        AS_CASE([[$host_os]],dnl
+          [[*linux*]],[[CPU_COUNT=`$EGREP -e '^processor' -c /proc/cpuinfo 2>/dev/null` || CPU_COUNT="0"]],dnl
+          [[*darwin*]],[[CPU_COUNT=`system_profiler SPHardwareDataType 2>/dev/null | $EGREP -i -e 'number of cores:'|cut -d : -f 2 -s|tr -d ' '` || CPU_COUNT="0"]],dnl
+          [[freebsd*]],[[CPU_COUNT=`dmesg 2>/dev/null| $EGREP -e '^cpu@<:@0-9@:>@+: '|sort -u|$EGREP -e '^' -c` || CPU_COUNT="0"]],dnl
+          [[netbsd*]], [[CPU_COUNT=`command -v cpuctl >/dev/null 2>&1 && cpuctl list 2>/dev/null| $EGREP -e '^@<:@0-9@:>@+ .* online ' -c` || \
+                           CPU_COUNT=`dmesg 2>/dev/null| $EGREP -e '^cpu@<:@0-9@:>@+ at'|sort -u|$EGREP -e '^' -c` || CPU_COUNT="0"]],dnl
+          [[solaris*]],[[command -v kstat >/dev/null 2>&1 && CPU_COUNT=`kstat -m cpu_info -s state -p 2>/dev/null | $EGREP -c -e 'on-line'` || \
+                           CPU_COUNT=`kstat -m cpu_info 2>/dev/null | $EGREP -c -e 'module: cpu_info'` || CPU_COUNT="0"]],dnl
+          [[mingw*]],[AS_IF([[CPU_COUNT=`reg query 'HKLM\\Hardware\\Description\\System\\CentralProcessor' 2>/dev/null | $EGREP -e '\\\\@<:@0-9@:>@+$' -c`]],dnl
+                        [[: # empty]],[[test "$NUMBER_OF_PROCESSORS" -gt "0" 2>/dev/null && CPU_COUNT="$NUMBER_OF_PROCESSORS"]])],dnl
+          [[msys*]],[[test "$NUMBER_OF_PROCESSORS" -gt "0" 2>/dev/null && CPU_COUNT="$NUMBER_OF_PROCESSORS"]],dnl
+          [[cygwin*]],[[test "$NUMBER_OF_PROCESSORS" -gt "0" 2>/dev/null && CPU_COUNT="$NUMBER_OF_PROCESSORS"]]dnl
+        )dnl
+      ])dnl
+
+      AS_IF([[test "x$CPU_COUNT" != "x0" && test "$CPU_COUNT" -gt 0 2>/dev/null]],[dnl
+          AC_MSG_RESULT([[$CPU_COUNT]])
+          m4_ifvaln([$1],[$1],)dnl
+        ],[dnl
+          m4_ifval([$2],[dnl
+            AS_UNSET([[CPU_COUNT]])
+            AC_MSG_RESULT([[unable to detect]])
+            $2
+          ], [dnl
+            CPU_COUNT="1"
+            AC_MSG_RESULT([[unable to detect (assuming 1)]])
+          ])dnl
+        ])dnl
+      ])dnl
diff --git a/m4/ax_cxx_compile_stdcxx.m4 b/m4/ax_cxx_compile_stdcxx.m4
index 8adc7656..2c18e49c 100644
--- a/m4/ax_cxx_compile_stdcxx.m4
+++ b/m4/ax_cxx_compile_stdcxx.m4
@@ -9,9 +9,9 @@
 # DESCRIPTION
 #
 #   Check for baseline language coverage in the compiler for the specified
-#   version of the C++ standard.  If necessary, add switches to CXX to
-#   enable support.  VERSION may be '11' (for the C++11 standard) or '14'
-#   (for the C++14 standard).
+#   version of the C++ standard.  If necessary, add switches to CXX and
+#   CXXCPP to enable support.  VERSION may be '11' (for the C++11 standard)
+#   or '14' (for the C++14 standard).
 #
 #   The second argument, if specified, indicates whether you insist on an
 #   extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
@@ -39,7 +39,7 @@
 #   and this notice are preserved.  This file is offered as-is, without any
 #   warranty.
 
-#serial 3
+#serial 4
 
 dnl  This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro
 dnl  (serial version number 13).
@@ -82,6 +82,9 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
          CXX="$ac_save_CXX"])
       if eval test x\$$cachevar = xyes; then
         CXX="$CXX $switch"
+        if test -n "$CXXCPP" ; then
+          CXXCPP="$CXXCPP $switch"
+        fi
         ac_success=yes
         break
       fi
@@ -105,6 +108,9 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
          CXX="$ac_save_CXX"])
       if eval test x\$$cachevar = xyes; then
         CXX="$CXX $switch"
+        if test -n "$CXXCPP" ; then
+          CXXCPP="$CXXCPP $switch"
+        fi
         ac_success=yes
         break
       fi
diff --git a/m4/ax_cxx_compile_stdcxx_11.m4 b/m4/ax_cxx_compile_stdcxx_11.m4
index b3d4bfda..0aadeafe 100644
--- a/m4/ax_cxx_compile_stdcxx_11.m4
+++ b/m4/ax_cxx_compile_stdcxx_11.m4
@@ -9,7 +9,8 @@
 # DESCRIPTION
 #
 #   Check for baseline language coverage in the compiler for the C++11
-#   standard; if necessary, add switches to CXX to enable support.
+#   standard; if necessary, add switches to CXX and CXXCPP to enable
+#   support.
 #
 #   This macro is a convenience alias for calling the AX_CXX_COMPILE_STDCXX
 #   macro with the version set to C++11.  The two optional arguments are
@@ -32,8 +33,7 @@
 #   and this notice are preserved. This file is offered as-is, without any
 #   warranty.
 
-#serial 15
-
-include([ax_cxx_compile_stdcxx.m4])
+#serial 17
 
+AX_REQUIRE_DEFINED([AX_CXX_COMPILE_STDCXX])
 AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [AX_CXX_COMPILE_STDCXX([11], [$1], [$2])])
diff --git a/m4/ax_gcc_builtin.m4 b/m4/ax_gcc_builtin.m4
index b28a91b1..54d87298 100644
--- a/m4/ax_gcc_builtin.m4
+++ b/m4/ax_gcc_builtin.m4
@@ -24,6 +24,7 @@
 #   The macro currently supports the following built-in functions:
 #
 #    __builtin_assume_aligned
+#    __builtin_bswap16
 #    __builtin_bswap32
 #    __builtin_bswap64
 #    __builtin_choose_expr
@@ -90,7 +91,7 @@
 #   and this notice are preserved.  This file is offered as-is, without any
 #   warranty.
 
-#serial 2
+#serial 3
 
 AC_DEFUN([AX_GCC_BUILTIN], [
     AS_VAR_PUSHDEF([ac_var], [ax_cv_have_$1])
@@ -99,6 +100,7 @@ AC_DEFUN([AX_GCC_BUILTIN], [
         AC_LINK_IFELSE([AC_LANG_PROGRAM([], [
             m4_case([$1],
                 [__builtin_assume_aligned], [$1("", 0)],
+                [__builtin_bswap16], [$1(0)],
                 [__builtin_bswap32], [$1(0)],
                 [__builtin_bswap64], [$1(0)],
                 [__builtin_choose_expr], [$1(0, 0, 0)],
diff --git a/m4/ax_prog_doxygen.m4 b/m4/ax_prog_doxygen.m4
index b2a899f3..e92c9e44 100644
--- a/m4/ax_prog_doxygen.m4
+++ b/m4/ax_prog_doxygen.m4
@@ -97,7 +97,7 @@
 #   and this notice are preserved. This file is offered as-is, without any
 #   warranty.
 
-#serial 19
+#serial 20
 
 ## ----------##
 ## Defaults. ##
@@ -553,7 +553,8 @@ doxygen-doc: doxygen-run \$(DX_PS_GOAL) \$(DX_PDF_GOAL)
 ]])dnl
 [DX_CLEANFILES = \\]
 m4_foreach([DX_i], [DX_loop],
-[[	\$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag \\
+[[	\$(DX_DOCDIR]DX_i[)/doxygen_sqlite3.db \\
+	\$(DX_DOCDIR]DX_i[)/\$(PACKAGE).tag \\
 ]])dnl
 [	-r \\
 	\$(DX_CLEAN_HTML) \\
diff --git a/m4/ax_pthread.m4 b/m4/ax_pthread.m4
index d218d1af..4c4051ea 100644
--- a/m4/ax_pthread.m4
+++ b/m4/ax_pthread.m4
@@ -82,7 +82,7 @@
 #   modified version of the Autoconf Macro, you may extend this special
 #   exception to the GPL to apply to your modified version as well.
 
-#serial 22
+#serial 23
 
 AU_ALIAS([ACX_PTHREAD], [AX_PTHREAD])
 AC_DEFUN([AX_PTHREAD], [
@@ -100,22 +100,22 @@ ax_pthread_ok=no
 # etcetera environment variables, and if threads linking works using
 # them:
 if test "x$PTHREAD_CFLAGS$PTHREAD_LIBS" != "x"; then
-	ax_pthread_save_CC="$CC"
-	ax_pthread_save_CFLAGS="$CFLAGS"
-	ax_pthread_save_LIBS="$LIBS"
-	AS_IF([test "x$PTHREAD_CC" != "x"], [CC="$PTHREAD_CC"])
-	CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
-	LIBS="$PTHREAD_LIBS $LIBS"
-	AC_MSG_CHECKING([for pthread_join using $CC $PTHREAD_CFLAGS $PTHREAD_LIBS])
-	AC_LINK_IFELSE([AC_LANG_CALL([], [pthread_join])], [ax_pthread_ok=yes])
-	AC_MSG_RESULT([$ax_pthread_ok])
-	if test "x$ax_pthread_ok" = "xno"; then
-		PTHREAD_LIBS=""
-		PTHREAD_CFLAGS=""
-	fi
-	CC="$ax_pthread_save_CC"
-	CFLAGS="$ax_pthread_save_CFLAGS"
-	LIBS="$ax_pthread_save_LIBS"
+        ax_pthread_save_CC="$CC"
+        ax_pthread_save_CFLAGS="$CFLAGS"
+        ax_pthread_save_LIBS="$LIBS"
+        AS_IF([test "x$PTHREAD_CC" != "x"], [CC="$PTHREAD_CC"])
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+        AC_MSG_CHECKING([for pthread_join using $CC $PTHREAD_CFLAGS $PTHREAD_LIBS])
+        AC_LINK_IFELSE([AC_LANG_CALL([], [pthread_join])], [ax_pthread_ok=yes])
+        AC_MSG_RESULT([$ax_pthread_ok])
+        if test "x$ax_pthread_ok" = "xno"; then
+                PTHREAD_LIBS=""
+                PTHREAD_CFLAGS=""
+        fi
+        CC="$ax_pthread_save_CC"
+        CFLAGS="$ax_pthread_save_CFLAGS"
+        LIBS="$ax_pthread_save_LIBS"
 fi
 
 # We must check for the threads library under a number of different
@@ -152,50 +152,50 @@ ax_pthread_flags="pthreads none -Kthread -pthread -pthreads -mthreads pthread --
 
 case $host_os in
 
-	freebsd*)
+        freebsd*)
 
-	# -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able)
-	# lthread: LinuxThreads port on FreeBSD (also preferred to -pthread)
+        # -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able)
+        # lthread: LinuxThreads port on FreeBSD (also preferred to -pthread)
 
-	ax_pthread_flags="-kthread lthread $ax_pthread_flags"
-	;;
+        ax_pthread_flags="-kthread lthread $ax_pthread_flags"
+        ;;
 
-	hpux*)
+        hpux*)
 
-	# From the cc(1) man page: "[-mt] Sets various -D flags to enable
-	# multi-threading and also sets -lpthread."
+        # From the cc(1) man page: "[-mt] Sets various -D flags to enable
+        # multi-threading and also sets -lpthread."
 
-	ax_pthread_flags="-mt -pthread pthread $ax_pthread_flags"
-	;;
+        ax_pthread_flags="-mt -pthread pthread $ax_pthread_flags"
+        ;;
 
-	openedition*)
+        openedition*)
 
-	# IBM z/OS requires a feature-test macro to be defined in order to
-	# enable POSIX threads at all, so give the user a hint if this is
-	# not set. (We don't define these ourselves, as they can affect
-	# other portions of the system API in unpredictable ways.)
+        # IBM z/OS requires a feature-test macro to be defined in order to
+        # enable POSIX threads at all, so give the user a hint if this is
+        # not set. (We don't define these ourselves, as they can affect
+        # other portions of the system API in unpredictable ways.)
 
-	AC_EGREP_CPP([AX_PTHREAD_ZOS_MISSING],
-	    [
-#	     if !defined(_OPEN_THREADS) && !defined(_UNIX03_THREADS)
-	     AX_PTHREAD_ZOS_MISSING
-#	     endif
-	    ],
-	    [AC_MSG_WARN([IBM z/OS requires -D_OPEN_THREADS or -D_UNIX03_THREADS to enable pthreads support.])])
-	;;
+        AC_EGREP_CPP([AX_PTHREAD_ZOS_MISSING],
+            [
+#            if !defined(_OPEN_THREADS) && !defined(_UNIX03_THREADS)
+             AX_PTHREAD_ZOS_MISSING
+#            endif
+            ],
+            [AC_MSG_WARN([IBM z/OS requires -D_OPEN_THREADS or -D_UNIX03_THREADS to enable pthreads support.])])
+        ;;
 
-	solaris*)
+        solaris*)
 
-	# On Solaris (at least, for some versions), libc contains stubbed
-	# (non-functional) versions of the pthreads routines, so link-based
-	# tests will erroneously succeed. (N.B.: The stubs are missing
-	# pthread_cleanup_push, or rather a function called by this macro,
-	# so we could check for that, but who knows whether they'll stub
-	# that too in a future libc.)  So we'll check first for the
-	# standard Solaris way of linking pthreads (-mt -lpthread).
+        # On Solaris (at least, for some versions), libc contains stubbed
+        # (non-functional) versions of the pthreads routines, so link-based
+        # tests will erroneously succeed. (N.B.: The stubs are missing
+        # pthread_cleanup_push, or rather a function called by this macro,
+        # so we could check for that, but who knows whether they'll stub
+        # that too in a future libc.)  So we'll check first for the
+        # standard Solaris way of linking pthreads (-mt -lpthread).
 
-	ax_pthread_flags="-mt,pthread pthread $ax_pthread_flags"
-	;;
+        ax_pthread_flags="-mt,pthread pthread $ax_pthread_flags"
+        ;;
 esac
 
 # GCC generally uses -pthread, or -pthreads on some platforms (e.g. SPARC)
@@ -208,17 +208,17 @@ AS_IF([test "x$GCC" = "xyes"],
 # correctly enabled
 
 case $host_os in
-	darwin* | hpux* | linux* | osf* | solaris*)
-	ax_pthread_check_macro="_REENTRANT"
-	;;
+        darwin* | hpux* | linux* | osf* | solaris*)
+        ax_pthread_check_macro="_REENTRANT"
+        ;;
 
-	aix* | freebsd*)
-	ax_pthread_check_macro="_THREAD_SAFE"
-	;;
+        aix*)
+        ax_pthread_check_macro="_THREAD_SAFE"
+        ;;
 
-	*)
-	ax_pthread_check_macro="--"
-	;;
+        *)
+        ax_pthread_check_macro="--"
+        ;;
 esac
 AS_IF([test "x$ax_pthread_check_macro" = "x--"],
       [ax_pthread_check_cond=0],
@@ -231,13 +231,13 @@ AC_CACHE_CHECK([whether $CC is Clang],
     [ax_cv_PTHREAD_CLANG=no
      # Note that Autoconf sets GCC=yes for Clang as well as GCC
      if test "x$GCC" = "xyes"; then
-	AC_EGREP_CPP([AX_PTHREAD_CC_IS_CLANG],
-	    [/* Note: Clang 2.7 lacks __clang_[a-z]+__ */
-#	     if defined(__clang__) && defined(__llvm__)
-	     AX_PTHREAD_CC_IS_CLANG
-#	     endif
-	    ],
-	    [ax_cv_PTHREAD_CLANG=yes])
+        AC_EGREP_CPP([AX_PTHREAD_CC_IS_CLANG],
+            [/* Note: Clang 2.7 lacks __clang_[a-z]+__ */
+#            if defined(__clang__) && defined(__llvm__)
+             AX_PTHREAD_CC_IS_CLANG
+#            endif
+            ],
+            [ax_cv_PTHREAD_CLANG=yes])
      fi
     ])
 ax_pthread_clang="$ax_cv_PTHREAD_CLANG"
@@ -249,222 +249,222 @@ ax_pthread_clang_warning=no
 
 if test "x$ax_pthread_clang" = "xyes"; then
 
-	# Clang takes -pthread; it has never supported any other flag
-
-	# (Note 1: This will need to be revisited if a system that Clang
-	# supports has POSIX threads in a separate library.  This tends not
-	# to be the way of modern systems, but it's conceivable.)
-
-	# (Note 2: On some systems, notably Darwin, -pthread is not needed
-	# to get POSIX threads support; the API is always present and
-	# active.  We could reasonably leave PTHREAD_CFLAGS empty.  But
-	# -pthread does define _REENTRANT, and while the Darwin headers
-	# ignore this macro, third-party headers might not.)
-
-	PTHREAD_CFLAGS="-pthread"
-	PTHREAD_LIBS=
-
-	ax_pthread_ok=yes
-
-	# However, older versions of Clang make a point of warning the user
-	# that, in an invocation where only linking and no compilation is
-	# taking place, the -pthread option has no effect ("argument unused
-	# during compilation").  They expect -pthread to be passed in only
-	# when source code is being compiled.
-	#
-	# Problem is, this is at odds with the way Automake and most other
-	# C build frameworks function, which is that the same flags used in
-	# compilation (CFLAGS) are also used in linking.  Many systems
-	# supported by AX_PTHREAD require exactly this for POSIX threads
-	# support, and in fact it is often not straightforward to specify a
-	# flag that is used only in the compilation phase and not in
-	# linking.  Such a scenario is extremely rare in practice.
-	#
-	# Even though use of the -pthread flag in linking would only print
-	# a warning, this can be a nuisance for well-run software projects
-	# that build with -Werror.  So if the active version of Clang has
-	# this misfeature, we search for an option to squash it.
-
-	AC_CACHE_CHECK([whether Clang needs flag to prevent "argument unused" warning when linking with -pthread],
-	    [ax_cv_PTHREAD_CLANG_NO_WARN_FLAG],
-	    [ax_cv_PTHREAD_CLANG_NO_WARN_FLAG=unknown
-	     # Create an alternate version of $ac_link that compiles and
-	     # links in two steps (.c -> .o, .o -> exe) instead of one
-	     # (.c -> exe), because the warning occurs only in the second
-	     # step
-	     ax_pthread_save_ac_link="$ac_link"
-	     ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g'
-	     ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"`
-	     ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)"
-	     ax_pthread_save_CFLAGS="$CFLAGS"
-	     for ax_pthread_try in '' -Qunused-arguments -Wno-unused-command-line-argument unknown; do
-		AS_IF([test "x$ax_pthread_try" = "xunknown"], [break])
-		CFLAGS="-Werror -Wunknown-warning-option $ax_pthread_try -pthread $ax_pthread_save_CFLAGS"
-		ac_link="$ax_pthread_save_ac_link"
-		AC_LINK_IFELSE([AC_LANG_SOURCE([[int main(void){return 0;}]])],
-		    [ac_link="$ax_pthread_2step_ac_link"
-		     AC_LINK_IFELSE([AC_LANG_SOURCE([[int main(void){return 0;}]])],
-			 [break])
-		    ])
-	     done
-	     ac_link="$ax_pthread_save_ac_link"
-	     CFLAGS="$ax_pthread_save_CFLAGS"
-	     AS_IF([test "x$ax_pthread_try" = "x"], [ax_pthread_try=no])
-	     ax_cv_PTHREAD_CLANG_NO_WARN_FLAG="$ax_pthread_try"
-	    ])
-
-	case "$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG" in
-		no | unknown) ;;
-		*) PTHREAD_CFLAGS="$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG $PTHREAD_CFLAGS" ;;
-	esac
+        # Clang takes -pthread; it has never supported any other flag
+
+        # (Note 1: This will need to be revisited if a system that Clang
+        # supports has POSIX threads in a separate library.  This tends not
+        # to be the way of modern systems, but it's conceivable.)
+
+        # (Note 2: On some systems, notably Darwin, -pthread is not needed
+        # to get POSIX threads support; the API is always present and
+        # active.  We could reasonably leave PTHREAD_CFLAGS empty.  But
+        # -pthread does define _REENTRANT, and while the Darwin headers
+        # ignore this macro, third-party headers might not.)
+
+        PTHREAD_CFLAGS="-pthread"
+        PTHREAD_LIBS=
+
+        ax_pthread_ok=yes
+
+        # However, older versions of Clang make a point of warning the user
+        # that, in an invocation where only linking and no compilation is
+        # taking place, the -pthread option has no effect ("argument unused
+        # during compilation").  They expect -pthread to be passed in only
+        # when source code is being compiled.
+        #
+        # Problem is, this is at odds with the way Automake and most other
+        # C build frameworks function, which is that the same flags used in
+        # compilation (CFLAGS) are also used in linking.  Many systems
+        # supported by AX_PTHREAD require exactly this for POSIX threads
+        # support, and in fact it is often not straightforward to specify a
+        # flag that is used only in the compilation phase and not in
+        # linking.  Such a scenario is extremely rare in practice.
+        #
+        # Even though use of the -pthread flag in linking would only print
+        # a warning, this can be a nuisance for well-run software projects
+        # that build with -Werror.  So if the active version of Clang has
+        # this misfeature, we search for an option to squash it.
+
+        AC_CACHE_CHECK([whether Clang needs flag to prevent "argument unused" warning when linking with -pthread],
+            [ax_cv_PTHREAD_CLANG_NO_WARN_FLAG],
+            [ax_cv_PTHREAD_CLANG_NO_WARN_FLAG=unknown
+             # Create an alternate version of $ac_link that compiles and
+             # links in two steps (.c -> .o, .o -> exe) instead of one
+             # (.c -> exe), because the warning occurs only in the second
+             # step
+             ax_pthread_save_ac_link="$ac_link"
+             ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g'
+             ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"`
+             ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)"
+             ax_pthread_save_CFLAGS="$CFLAGS"
+             for ax_pthread_try in '' -Qunused-arguments -Wno-unused-command-line-argument unknown; do
+                AS_IF([test "x$ax_pthread_try" = "xunknown"], [break])
+                CFLAGS="-Werror -Wunknown-warning-option $ax_pthread_try -pthread $ax_pthread_save_CFLAGS"
+                ac_link="$ax_pthread_save_ac_link"
+                AC_LINK_IFELSE([AC_LANG_SOURCE([[int main(void){return 0;}]])],
+                    [ac_link="$ax_pthread_2step_ac_link"
+                     AC_LINK_IFELSE([AC_LANG_SOURCE([[int main(void){return 0;}]])],
+                         [break])
+                    ])
+             done
+             ac_link="$ax_pthread_save_ac_link"
+             CFLAGS="$ax_pthread_save_CFLAGS"
+             AS_IF([test "x$ax_pthread_try" = "x"], [ax_pthread_try=no])
+             ax_cv_PTHREAD_CLANG_NO_WARN_FLAG="$ax_pthread_try"
+            ])
+
+        case "$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG" in
+                no | unknown) ;;
+                *) PTHREAD_CFLAGS="$ax_cv_PTHREAD_CLANG_NO_WARN_FLAG $PTHREAD_CFLAGS" ;;
+        esac
 
 fi # $ax_pthread_clang = yes
 
 if test "x$ax_pthread_ok" = "xno"; then
 for ax_pthread_try_flag in $ax_pthread_flags; do
 
-	case $ax_pthread_try_flag in
-		none)
-		AC_MSG_CHECKING([whether pthreads work without any flags])
-		;;
-
-		-mt,pthread)
-		AC_MSG_CHECKING([whether pthreads work with -mt -lpthread])
-		PTHREAD_CFLAGS="-mt"
-		PTHREAD_LIBS="-lpthread"
-		;;
-
-		-*)
-		AC_MSG_CHECKING([whether pthreads work with $ax_pthread_try_flag])
-		PTHREAD_CFLAGS="$ax_pthread_try_flag"
-		;;
-
-		pthread-config)
-		AC_CHECK_PROG([ax_pthread_config], [pthread-config], [yes], [no])
-		AS_IF([test "x$ax_pthread_config" = "xno"], [continue])
-		PTHREAD_CFLAGS="`pthread-config --cflags`"
-		PTHREAD_LIBS="`pthread-config --ldflags` `pthread-config --libs`"
-		;;
-
-		*)
-		AC_MSG_CHECKING([for the pthreads library -l$ax_pthread_try_flag])
-		PTHREAD_LIBS="-l$ax_pthread_try_flag"
-		;;
-	esac
-
-	ax_pthread_save_CFLAGS="$CFLAGS"
-	ax_pthread_save_LIBS="$LIBS"
-	CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
-	LIBS="$PTHREAD_LIBS $LIBS"
-
-	# Check for various functions.  We must include pthread.h,
-	# since some functions may be macros.  (On the Sequent, we
-	# need a special flag -Kthread to make this header compile.)
-	# We check for pthread_join because it is in -lpthread on IRIX
-	# while pthread_create is in libc.  We check for pthread_attr_init
-	# due to DEC craziness with -lpthreads.  We check for
-	# pthread_cleanup_push because it is one of the few pthread
-	# functions on Solaris that doesn't have a non-functional libc stub.
-	# We try pthread_create on general principles.
-
-	AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>
-#			if $ax_pthread_check_cond
-#			 error "$ax_pthread_check_macro must be defined"
-#			endif
-			static void routine(void *a) { a = 0; }
-			static void *start_routine(void *a) { return a; }],
-		       [pthread_t th; pthread_attr_t attr;
-			pthread_create(&th, 0, start_routine, 0);
-			pthread_join(th, 0);
-			pthread_attr_init(&attr);
-			pthread_cleanup_push(routine, 0);
-			pthread_cleanup_pop(0) /* ; */])],
-	    [ax_pthread_ok=yes],
-	    [])
-
-	CFLAGS="$ax_pthread_save_CFLAGS"
-	LIBS="$ax_pthread_save_LIBS"
-
-	AC_MSG_RESULT([$ax_pthread_ok])
-	AS_IF([test "x$ax_pthread_ok" = "xyes"], [break])
-
-	PTHREAD_LIBS=""
-	PTHREAD_CFLAGS=""
+        case $ax_pthread_try_flag in
+                none)
+                AC_MSG_CHECKING([whether pthreads work without any flags])
+                ;;
+
+                -mt,pthread)
+                AC_MSG_CHECKING([whether pthreads work with -mt -lpthread])
+                PTHREAD_CFLAGS="-mt"
+                PTHREAD_LIBS="-lpthread"
+                ;;
+
+                -*)
+                AC_MSG_CHECKING([whether pthreads work with $ax_pthread_try_flag])
+                PTHREAD_CFLAGS="$ax_pthread_try_flag"
+                ;;
+
+                pthread-config)
+                AC_CHECK_PROG([ax_pthread_config], [pthread-config], [yes], [no])
+                AS_IF([test "x$ax_pthread_config" = "xno"], [continue])
+                PTHREAD_CFLAGS="`pthread-config --cflags`"
+                PTHREAD_LIBS="`pthread-config --ldflags` `pthread-config --libs`"
+                ;;
+
+                *)
+                AC_MSG_CHECKING([for the pthreads library -l$ax_pthread_try_flag])
+                PTHREAD_LIBS="-l$ax_pthread_try_flag"
+                ;;
+        esac
+
+        ax_pthread_save_CFLAGS="$CFLAGS"
+        ax_pthread_save_LIBS="$LIBS"
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+
+        # Check for various functions.  We must include pthread.h,
+        # since some functions may be macros.  (On the Sequent, we
+        # need a special flag -Kthread to make this header compile.)
+        # We check for pthread_join because it is in -lpthread on IRIX
+        # while pthread_create is in libc.  We check for pthread_attr_init
+        # due to DEC craziness with -lpthreads.  We check for
+        # pthread_cleanup_push because it is one of the few pthread
+        # functions on Solaris that doesn't have a non-functional libc stub.
+        # We try pthread_create on general principles.
+
+        AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>
+#                       if $ax_pthread_check_cond
+#                        error "$ax_pthread_check_macro must be defined"
+#                       endif
+                        static void routine(void *a) { a = 0; }
+                        static void *start_routine(void *a) { return a; }],
+                       [pthread_t th; pthread_attr_t attr;
+                        pthread_create(&th, 0, start_routine, 0);
+                        pthread_join(th, 0);
+                        pthread_attr_init(&attr);
+                        pthread_cleanup_push(routine, 0);
+                        pthread_cleanup_pop(0) /* ; */])],
+            [ax_pthread_ok=yes],
+            [])
+
+        CFLAGS="$ax_pthread_save_CFLAGS"
+        LIBS="$ax_pthread_save_LIBS"
+
+        AC_MSG_RESULT([$ax_pthread_ok])
+        AS_IF([test "x$ax_pthread_ok" = "xyes"], [break])
+
+        PTHREAD_LIBS=""
+        PTHREAD_CFLAGS=""
 done
 fi
 
 # Various other checks:
 if test "x$ax_pthread_ok" = "xyes"; then
-	ax_pthread_save_CFLAGS="$CFLAGS"
-	ax_pthread_save_LIBS="$LIBS"
-	CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
-	LIBS="$PTHREAD_LIBS $LIBS"
-
-	# Detect AIX lossage: JOINABLE attribute is called UNDETACHED.
-	AC_CACHE_CHECK([for joinable pthread attribute],
-	    [ax_cv_PTHREAD_JOINABLE_ATTR],
-	    [ax_cv_PTHREAD_JOINABLE_ATTR=unknown
-	     for ax_pthread_attr in PTHREAD_CREATE_JOINABLE PTHREAD_CREATE_UNDETACHED; do
-		 AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>],
-						 [int attr = $ax_pthread_attr; return attr /* ; */])],
-				[ax_cv_PTHREAD_JOINABLE_ATTR=$ax_pthread_attr; break],
-				[])
-	     done
-	    ])
-	AS_IF([test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xunknown" && \
-	       test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xPTHREAD_CREATE_JOINABLE" && \
-	       test "x$ax_pthread_joinable_attr_defined" != "xyes"],
-	      [AC_DEFINE_UNQUOTED([PTHREAD_CREATE_JOINABLE],
-				  [$ax_cv_PTHREAD_JOINABLE_ATTR],
-				  [Define to necessary symbol if this constant
-				   uses a non-standard name on your system.])
-	       ax_pthread_joinable_attr_defined=yes
-	      ])
-
-	AC_CACHE_CHECK([whether more special flags are required for pthreads],
-	    [ax_cv_PTHREAD_SPECIAL_FLAGS],
-	    [ax_cv_PTHREAD_SPECIAL_FLAGS=no
-	     case $host_os in
-	     solaris*)
-	     ax_cv_PTHREAD_SPECIAL_FLAGS="-D_POSIX_PTHREAD_SEMANTICS"
-	     ;;
-	     esac
-	    ])
-	AS_IF([test "x$ax_cv_PTHREAD_SPECIAL_FLAGS" != "xno" && \
-	       test "x$ax_pthread_special_flags_added" != "xyes"],
-	      [PTHREAD_CFLAGS="$ax_cv_PTHREAD_SPECIAL_FLAGS $PTHREAD_CFLAGS"
-	       ax_pthread_special_flags_added=yes])
-
-	AC_CACHE_CHECK([for PTHREAD_PRIO_INHERIT],
-	    [ax_cv_PTHREAD_PRIO_INHERIT],
-	    [AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <pthread.h>]],
-					     [[int i = PTHREAD_PRIO_INHERIT;]])],
-			    [ax_cv_PTHREAD_PRIO_INHERIT=yes],
-			    [ax_cv_PTHREAD_PRIO_INHERIT=no])
-	    ])
-	AS_IF([test "x$ax_cv_PTHREAD_PRIO_INHERIT" = "xyes" && \
-	       test "x$ax_pthread_prio_inherit_defined" != "xyes"],
-	      [AC_DEFINE([HAVE_PTHREAD_PRIO_INHERIT], [1], [Have PTHREAD_PRIO_INHERIT.])
-	       ax_pthread_prio_inherit_defined=yes
-	      ])
-
-	CFLAGS="$ax_pthread_save_CFLAGS"
-	LIBS="$ax_pthread_save_LIBS"
-
-	# More AIX lossage: compile with *_r variant
-	if test "x$GCC" != "xyes"; then
-	    case $host_os in
-		aix*)
-		AS_CASE(["x/$CC"],
-		    [x*/c89|x*/c89_128|x*/c99|x*/c99_128|x*/cc|x*/cc128|x*/xlc|x*/xlc_v6|x*/xlc128|x*/xlc128_v6],
-		    [#handle absolute path differently from PATH based program lookup
-		     AS_CASE(["x$CC"],
-			 [x/*],
-			 [AS_IF([AS_EXECUTABLE_P([${CC}_r])],[PTHREAD_CC="${CC}_r"])],
-			 [AC_CHECK_PROGS([PTHREAD_CC],[${CC}_r],[$CC])])])
-		;;
-	    esac
-	fi
+        ax_pthread_save_CFLAGS="$CFLAGS"
+        ax_pthread_save_LIBS="$LIBS"
+        CFLAGS="$CFLAGS $PTHREAD_CFLAGS"
+        LIBS="$PTHREAD_LIBS $LIBS"
+
+        # Detect AIX lossage: JOINABLE attribute is called UNDETACHED.
+        AC_CACHE_CHECK([for joinable pthread attribute],
+            [ax_cv_PTHREAD_JOINABLE_ATTR],
+            [ax_cv_PTHREAD_JOINABLE_ATTR=unknown
+             for ax_pthread_attr in PTHREAD_CREATE_JOINABLE PTHREAD_CREATE_UNDETACHED; do
+                 AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pthread.h>],
+                                                 [int attr = $ax_pthread_attr; return attr /* ; */])],
+                                [ax_cv_PTHREAD_JOINABLE_ATTR=$ax_pthread_attr; break],
+                                [])
+             done
+            ])
+        AS_IF([test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xunknown" && \
+               test "x$ax_cv_PTHREAD_JOINABLE_ATTR" != "xPTHREAD_CREATE_JOINABLE" && \
+               test "x$ax_pthread_joinable_attr_defined" != "xyes"],
+              [AC_DEFINE_UNQUOTED([PTHREAD_CREATE_JOINABLE],
+                                  [$ax_cv_PTHREAD_JOINABLE_ATTR],
+                                  [Define to necessary symbol if this constant
+                                   uses a non-standard name on your system.])
+               ax_pthread_joinable_attr_defined=yes
+              ])
+
+        AC_CACHE_CHECK([whether more special flags are required for pthreads],
+            [ax_cv_PTHREAD_SPECIAL_FLAGS],
+            [ax_cv_PTHREAD_SPECIAL_FLAGS=no
+             case $host_os in
+             solaris*)
+             ax_cv_PTHREAD_SPECIAL_FLAGS="-D_POSIX_PTHREAD_SEMANTICS"
+             ;;
+             esac
+            ])
+        AS_IF([test "x$ax_cv_PTHREAD_SPECIAL_FLAGS" != "xno" && \
+               test "x$ax_pthread_special_flags_added" != "xyes"],
+              [PTHREAD_CFLAGS="$ax_cv_PTHREAD_SPECIAL_FLAGS $PTHREAD_CFLAGS"
+               ax_pthread_special_flags_added=yes])
+
+        AC_CACHE_CHECK([for PTHREAD_PRIO_INHERIT],
+            [ax_cv_PTHREAD_PRIO_INHERIT],
+            [AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <pthread.h>]],
+                                             [[int i = PTHREAD_PRIO_INHERIT;]])],
+                            [ax_cv_PTHREAD_PRIO_INHERIT=yes],
+                            [ax_cv_PTHREAD_PRIO_INHERIT=no])
+            ])
+        AS_IF([test "x$ax_cv_PTHREAD_PRIO_INHERIT" = "xyes" && \
+               test "x$ax_pthread_prio_inherit_defined" != "xyes"],
+              [AC_DEFINE([HAVE_PTHREAD_PRIO_INHERIT], [1], [Have PTHREAD_PRIO_INHERIT.])
+               ax_pthread_prio_inherit_defined=yes
+              ])
+
+        CFLAGS="$ax_pthread_save_CFLAGS"
+        LIBS="$ax_pthread_save_LIBS"
+
+        # More AIX lossage: compile with *_r variant
+        if test "x$GCC" != "xyes"; then
+            case $host_os in
+                aix*)
+                AS_CASE(["x/$CC"],
+                    [x*/c89|x*/c89_128|x*/c99|x*/c99_128|x*/cc|x*/cc128|x*/xlc|x*/xlc_v6|x*/xlc128|x*/xlc128_v6],
+                    [#handle absolute path differently from PATH based program lookup
+                     AS_CASE(["x$CC"],
+                         [x/*],
+                         [AS_IF([AS_EXECUTABLE_P([${CC}_r])],[PTHREAD_CC="${CC}_r"])],
+                         [AC_CHECK_PROGS([PTHREAD_CC],[${CC}_r],[$CC])])])
+                ;;
+            esac
+        fi
 fi
 
 test -n "$PTHREAD_CC" || PTHREAD_CC="$CC"
@@ -475,11 +475,11 @@ AC_SUBST([PTHREAD_CC])
 
 # Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
 if test "x$ax_pthread_ok" = "xyes"; then
-	ifelse([$1],,[AC_DEFINE([HAVE_PTHREAD],[1],[Define if you have POSIX threads libraries and header files.])],[$1])
-	:
+        ifelse([$1],,[AC_DEFINE([HAVE_PTHREAD],[1],[Define if you have POSIX threads libraries and header files.])],[$1])
+        :
 else
-	ax_pthread_ok=no
-	$2
+        ax_pthread_ok=no
+        $2
 fi
 AC_LANG_POP
 ])dnl AX_PTHREAD

From 20a2cdb29709962532438097bc2a86511c1390d1 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 15:01:52 -0500
Subject: [PATCH 08/44] AX_COUNT_CPUS's signature has changed.

---
 configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure.ac b/configure.ac
index d23c5bab..0cff9512 100644
--- a/configure.ac
+++ b/configure.ac
@@ -59,7 +59,7 @@ AM_INIT_AUTOMAKE([
 AC_USE_SYSTEM_EXTENSIONS
 
 # Determine how many CPUs we have on the build machine.
-AX_COUNT_CPUS
+AX_COUNT_CPUS([], [])
 AC_SUBST([CPU_COUNT])
 
 # Set up the maintainer compiler flags.

From 3f7e07ebc84b76c822a222c3d14cc159b3ce662e Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 15:44:44 -0500
Subject: [PATCH 09/44] Not finding Argp needs to be a fatal configure error at
 this time.

---
 configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure.ac b/configure.ac
index 0cff9512..2fbbb7a9 100644
--- a/configure.ac
+++ b/configure.ac
@@ -390,7 +390,7 @@ AC_CHECK_DECLS([std::to_string(int)],
 				],
 				[], [#include <string>])
 
-AC_SEARCH_LIBS([argp_parse],[argp])
+AC_SEARCH_LIBS([argp_parse], [argp], [], [AC_MSG_ERROR([cannot find the GNU Argp library or equivalent.])])
 
 AC_CHECK_FUNCS([sched_setaffinity])
 

From c82b4af1645a5bf83d6081a3ef9eefb552afd5c1 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 15:54:44 -0500
Subject: [PATCH 10/44] Moved function attributes from aligned_alloc()
 definition to declaration.

---
 src/ResizableArray.h | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ResizableArray.h b/src/ResizableArray.h
index 3a3c75f6..9c7ccc23 100644
--- a/src/ResizableArray.h
+++ b/src/ResizableArray.h
@@ -27,7 +27,8 @@
 // Nothing to do.
 #elif HAVE_POSIX_MEMALIGN
 // Create a thin wrapper around posix_memalign().
-inline void* aligned_alloc(size_t algn, size_t size) ATTR_ALLOC_SIZE(2) ATTR_MALLOC { void *p=0; posix_memalign(&p, algn, size); return p; };
+inline void* aligned_alloc(size_t algn, size_t size) ATTR_ALLOC_SIZE(2) ATTR_MALLOC;
+inline void* aligned_alloc(size_t algn, size_t size) { void *p=0; posix_memalign(&p, algn, size); return p; };
 #else
 #error "Could not find aligned memory allocator."
 #endif

From fb57f6cca538efc6b356af4ae3f49ec306e2243b Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 19:38:05 -0500
Subject: [PATCH 11/44] Travis matrix experiment.

---
 .travis.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cd7f5a3f..d7467338 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,10 +1,12 @@
 language: cpp
-sudo: required
-dist: trusty
 
-os:
- - osx
- - linux
+matrix:
+	include:
+		- os: osx
+ 	  	  osx_image: xcode8
+		- os: linux
+		  dist: trusty
+		  sudo: required
  
 compiler:
   - clang

From 1c9d76e04f6855e8f82e03c8d347d68b2cf2ae4b Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 19:40:18 -0500
Subject: [PATCH 12/44] Travis matrix experiment.

---
 .travis.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index d7467338..f4796ca8 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,12 +1,12 @@
 language: cpp
 
 matrix:
-	include:
-		- os: osx
- 	  	  osx_image: xcode8
-		- os: linux
-		  dist: trusty
-		  sudo: required
+    include:
+        - os: osx
+          osx_image: xcode8
+        - os: linux
+          dist: trusty
+          sudo: required
  
 compiler:
   - clang

From e68ce7be686d56d5f0a5f16429073239f678ceb8 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 19:55:16 -0500
Subject: [PATCH 13/44] Travis matrix experiment.

---
 .travis.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f4796ca8..d0fe1020 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,10 +7,14 @@ matrix:
         - os: linux
           dist: trusty
           sudo: required
- 
-compiler:
-  - clang
-  - gcc
+          compiler: gcc
+        - os: linux
+          dist: trusty
+          sudo: required
+          compiler: clang
+#compiler:
+#  - clang
+#  - gcc
 
 before_install:
  - if [ $TRAVIS_OS_NAME == osx ]; then brew update; fi

From e88173bf3102904f8c4f40942bcde047e4e72efd Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 20:04:59 -0500
Subject: [PATCH 14/44] Travis matrix experiment.

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d0fe1020..de1c0f02 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,9 @@ language: cpp
 matrix:
     include:
         - os: osx
-          osx_image: xcode8
+          osx_image:
+              - xcode8
+              - beta-xcode6.1
         - os: linux
           dist: trusty
           sudo: required

From 2655269af3225bc83622a7be57adece9e0c51b49 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 20:07:02 -0500
Subject: [PATCH 15/44] Travis matrix experiment.

---
 .travis.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index de1c0f02..c69af7a3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,9 +3,7 @@ language: cpp
 matrix:
     include:
         - os: osx
-          osx_image:
-              - xcode8
-              - beta-xcode6.1
+          osx_image: [xcode8, beta-xcode6.1]
         - os: linux
           dist: trusty
           sudo: required

From ef97f3dba9e4caab934023728eaaf81f7337efd3 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 20:08:25 -0500
Subject: [PATCH 16/44] Travis matrix experiment.

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index c69af7a3..357249fc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,9 @@ language: cpp
 matrix:
     include:
         - os: osx
-          osx_image: [xcode8, beta-xcode6.1]
+          osx_image: beta-xcode6.1
+        - os: osx
+          osx_image: xcode8
         - os: linux
           dist: trusty
           sudo: required

From 745c436244337811af47a25ee61cb60469cf6996 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Sun, 2 Oct 2016 20:47:32 -0500
Subject: [PATCH 17/44] Don't throw exception if PCRE2 regex JIT compile
 indicates JIT is not available.

---
 src/FileScannerPCRE2.cpp | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/FileScannerPCRE2.cpp b/src/FileScannerPCRE2.cpp
index 5166722d..4b89e920 100644
--- a/src/FileScannerPCRE2.cpp
+++ b/src/FileScannerPCRE2.cpp
@@ -141,9 +141,18 @@ FileScannerPCRE2::FileScannerPCRE2(sync_queue<FileID> &in_queue,
 
 	if(jit_retval != 0)
 	{
-		// JIT compilation error.
-		pcre2_code_free(m_pcre2_regex);
-		throw FileScannerException(std::string("PCRE2 JIT compilation error: ") + PCRE2ErrorCodeToErrorString(jit_retval));
+		// Was it a real error, or does the PCRE2 lib not have JIT compiled in?
+		if(jit_retval == PCRE2_ERROR_JIT_BADOPTION)
+		{
+			// No JIT support.
+			LOG(INFO) << "No PCRE2 JIT support: " << PCRE2ErrorCodeToErrorString(jit_retval);
+		}
+		else
+		{
+			// JIT compilation error.
+			pcre2_code_free(m_pcre2_regex);
+			throw FileScannerException(std::string("PCRE2 JIT compilation error: ") + PCRE2ErrorCodeToErrorString(jit_retval));
+		}
 	}
 
 	// Only allow the one callout we use internally, no user callouts.

From a09bbc07b79aae9e2d563b3e8304d3d3d3a2be1f Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Mon, 3 Oct 2016 08:44:30 -0500
Subject: [PATCH 18/44] Added XCode 7.1.

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 357249fc..6c07689c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,8 @@ matrix:
     include:
         - os: osx
           osx_image: beta-xcode6.1
+        - os: osx
+          osx_image: xcode7.1
         - os: osx
           osx_image: xcode8
         - os: linux

From 040e5f5d0ab163168865ca5db350826df82571b0 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Mon, 3 Oct 2016 20:19:50 -0500
Subject: [PATCH 19/44] Added "stty raw" as part of invoking script utility to
 prevent tab expansion as seen in issue #103.

---
 configure.ac     | 4 ++--
 tests/atlocal.in | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/configure.ac b/configure.ac
index 2fbbb7a9..73c39921 100644
--- a/configure.ac
+++ b/configure.ac
@@ -128,14 +128,14 @@ AS_IF([ test "x$ac_path_ESED_found" = "x:" ],
 # try to sort it out here.
 AC_PATH_PROG([PROG_SCRIPT], [script], [:])
 AC_MSG_CHECKING([$PROG_SCRIPT's command line type])
-AS_IF([$PROG_SCRIPT -qfc "echo hello" /dev/null > /dev/null 2>&1],
+AS_IF([$PROG_SCRIPT -qfc "stty raw && echo hello" /dev/null > /dev/null 2>&1],
 		[
 		AC_SUBST([PROG_SCRIPT_TYPE], [linux])
 		AC_SUBST([PROG_SCRIPT_PRE_TEXT], ['-qfc'])
 		AC_SUBST([PROG_SCRIPT_POST_TEXT], ['/dev/null'])
 		AC_MSG_RESULT([Linux style])
 		],
-      [$PROG_SCRIPT -q /dev/null echo "hello" > /dev/null 2>&1],
+      [$PROG_SCRIPT -q /dev/null stty raw && echo "hello" > /dev/null 2>&1],
 		[
 		AC_SUBST([PROG_SCRIPT_TYPE], [bsd])
 		AC_SUBST([PROG_SCRIPT_PRE_TEXT], ['-q /dev/null'])
diff --git a/tests/atlocal.in b/tests/atlocal.in
index d80fb2f8..9b76c77b 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -213,8 +213,8 @@ ASX_SCRIPT ()
 {
 	# Note: '\r' removal in here because script outputs \r\n's, even on Linuxes.
 	case $PROG_SCRIPT_TYPE in
-		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$*" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "${@}" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT stty raw && "${@}" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From 971372bd0192f285609c0477a58df34a21b697be Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 08:07:12 -0500
Subject: [PATCH 20/44] Interim.

---
 configure.ac     | 2 +-
 tests/atlocal.in | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/configure.ac b/configure.ac
index 73c39921..8008d92e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -135,7 +135,7 @@ AS_IF([$PROG_SCRIPT -qfc "stty raw && echo hello" /dev/null > /dev/null 2>&1],
 		AC_SUBST([PROG_SCRIPT_POST_TEXT], ['/dev/null'])
 		AC_MSG_RESULT([Linux style])
 		],
-      [$PROG_SCRIPT -q /dev/null stty raw && echo "hello" > /dev/null 2>&1],
+      [stty raw && $PROG_SCRIPT -q /dev/null echo "hello" > /dev/null 2>&1],
 		[
 		AC_SUBST([PROG_SCRIPT_TYPE], [bsd])
 		AC_SUBST([PROG_SCRIPT_PRE_TEXT], ['-q /dev/null'])
diff --git a/tests/atlocal.in b/tests/atlocal.in
index 9b76c77b..81b7451e 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -214,7 +214,7 @@ ASX_SCRIPT ()
 	# Note: '\r' removal in here because script outputs \r\n's, even on Linuxes.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT stty raw && "${@}" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) stty raw && $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "${@}" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From ef3375a07c8956ab8c27296ffe029c11ac4e526c Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 08:24:41 -0500
Subject: [PATCH 21/44] script vs. tty settings should be fixed for BSDs now.

---
 configure.ac     | 2 +-
 tests/atlocal.in | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/configure.ac b/configure.ac
index 8008d92e..1f9256b0 100644
--- a/configure.ac
+++ b/configure.ac
@@ -135,7 +135,7 @@ AS_IF([$PROG_SCRIPT -qfc "stty raw && echo hello" /dev/null > /dev/null 2>&1],
 		AC_SUBST([PROG_SCRIPT_POST_TEXT], ['/dev/null'])
 		AC_MSG_RESULT([Linux style])
 		],
-      [stty raw && $PROG_SCRIPT -q /dev/null echo "hello" > /dev/null 2>&1],
+      [$PROG_SCRIPT -q /dev/null $SHELL -c 'stty raw && echo "hello"' > /dev/null 2>&1],
 		[
 		AC_SUBST([PROG_SCRIPT_TYPE], [bsd])
 		AC_SUBST([PROG_SCRIPT_PRE_TEXT], ['-q /dev/null'])
diff --git a/tests/atlocal.in b/tests/atlocal.in
index 81b7451e..f61bc97e 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -214,7 +214,7 @@ ASX_SCRIPT ()
 	# Note: '\r' removal in here because script outputs \r\n's, even on Linuxes.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) stty raw && $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "${@}" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From 998f6b19c3133479dd6628bb1188f05102eaa68c Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 08:42:59 -0500
Subject: [PATCH 22/44] Another try.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index f61bc97e..c876365f 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -214,7 +214,7 @@ ASX_SCRIPT ()
 	# Note: '\r' removal in here because script outputs \r\n's, even on Linuxes.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && "${@}"" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From ee37485f0d280caadb3cf6f4a6e0c7b15e70bc1d Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 09:17:07 -0500
Subject: [PATCH 23/44] Another BSD fix.  Works on PC-BSD.

---
 tests/atlocal.in | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index c876365f..37802792 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -212,9 +212,18 @@ get_system_info()
 ASX_SCRIPT ()
 {
 	# Note: '\r' removal in here because script outputs \r\n's, even on Linuxes.
+	# @note The BSD case here seems to work for our current purposes, but I suspect it may fail if
+	#       we pass in args with nontrivial quoting or escapes.  E.g., if you './run -x -d' the "--[no]column tests",
+	#       you'll see this:
+	#         ../../tests/file_presentation.at:59: { ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } > stdout_tty
+	#         + ASX_SCRIPT ucg --noenv --cpp --nocolor --column do_something
+	#         + printf %s 'ucg --noenv --cpp --nocolor --column do_something'
+	#         + tr -d '\r'
+	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
+	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && "${@}"" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From 5a2ad5b329314490d0ba39d5f351740b15e921a6 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 20:14:09 -0500
Subject: [PATCH 24/44] Interim.

---
 tests/atlocal.in           |  4 +++-
 tests/file_presentation.at | 16 +++++++++-------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 37802792..45cd2e69 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -228,5 +228,7 @@ ASX_SCRIPT ()
 	esac
 }
 
-
+# Pipe output through this to convert to an ASCII+Hex text representation.
+# Useful for detecting differences in non-printing characters. 
+PROG_TOHEX='od -t ax1'
 
diff --git a/tests/file_presentation.at b/tests/file_presentation.at
index f47b6f6e..377fad97 100644
--- a/tests/file_presentation.at
+++ b/tests/file_presentation.at
@@ -56,8 +56,11 @@ AT_DATA([test_file.cpp.expected],[test_file.cpp
 4:2:	do_something();
 6:5:    do_something_else();
 ])
-AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } > stdout_tty], [0], [stdout], [stderr])
-AT_CHECK([diff test_file.cpp.expected stdout_tty], [0], [stdout], [stderr]) 
+
+AT_CHECK([cat test_file.cpp.expected | $PROG_TOHEX > test_file.cpp.expected.hex], [0])
+
+AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
+AT_CHECK([diff test_file.cpp.expected.hex stdout_tty], [0], [stdout], [stderr]) 
 
 
 # Check for nocolumn output to a TTY.
@@ -68,7 +71,7 @@ AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor --nocolumn 'do_something'],[0],
 ])
 
 # Check for default (nocolumn) output to a TTY.
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'do_something'],[0],
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'do_something'], [0],
 [test_file.cpp
 4:	do_something();
 6:    do_something_else();
@@ -121,17 +124,16 @@ efgh
 abcd
 ])
 
-AT_DATA([expout],
-[@<:@32;1m@<:@Ktest_file.cpp@<:@0m@<:@K
+AT_DATA([expout],[@<:@32;1m@<:@Ktest_file.cpp@<:@0m@<:@K
 @<:@33;1m@<:@K1@<:@0m@<:@K:a@<:@30;43;1m@<:@Kbc@<:@0m@<:@Kd
 @<:@33;1m@<:@K3@<:@0m@<:@K:a@<:@30;43;1m@<:@Kbc@<:@0m@<:@Kd
 ])
 
 # Check for color output to a TTY.
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --color 'bc'],[0],[expout])
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --color 'bc'], [0], [expout])
 
 # Check for nocolor to a TTY.
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'bc'],[0],
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'bc'], [0],
 [test_file.cpp
 1:abcd
 3:abcd

From 58550501e0930fe489688c348e8c1abc64fd6631 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 20:20:53 -0500
Subject: [PATCH 25/44] printf portability fix.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 45cd2e69..5943d0e2 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -222,7 +222,7 @@ ASX_SCRIPT ()
 	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	case $PROG_SCRIPT_TYPE in
-		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf "%q " "${@}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac

From 9f3c3946d315412413ed5cba52dafefdcd78b59b Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Tue, 4 Oct 2016 20:44:04 -0500
Subject: [PATCH 26/44] Interim.

---
 tests/file_presentation.at | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/tests/file_presentation.at b/tests/file_presentation.at
index 377fad97..73127a69 100644
--- a/tests/file_presentation.at
+++ b/tests/file_presentation.at
@@ -118,8 +118,7 @@ AT_CLEANUP
 #
 AT_SETUP([Color-vs-terminal tests])
 
-AT_DATA([test_file.cpp],
-[abcd
+AT_DATA([test_file.cpp],[abcd
 efgh
 abcd
 ])
@@ -133,13 +132,12 @@ AT_DATA([expout],[@<:@32;1m@<:@Ktest_file.cpp@<:@0m@<:@K
 AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --color 'bc'], [0], [expout])
 
 # Check for nocolor to a TTY.
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'bc'], [0],
-[test_file.cpp
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'bc'], [0], [test_file.cpp
 1:abcd
 3:abcd
 ])
 
 # Check for default (should be color).
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp 'bc'],[0],[expout])
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp 'bc'], [0], [expout])
 
 AT_CLEANUP

From da58316bdc03d9983e265805681d5dc3473661a6 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 08:33:09 -0500
Subject: [PATCH 27/44] script workaround for some OSX distro versions.

---
 tests/atlocal.in | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 5943d0e2..2c4e4103 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -221,9 +221,13 @@ ASX_SCRIPT ()
 	#         + tr -d '\r'
 	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
+	#
+	# @note On some OSX systems (which detect as having a bsd-style 'script' utility), the below will prefix
+	#       the output with '^D<backspace><backspace>' (hex 5e  44  08  08).  Not clear why.  Until we figure that out, just
+	#       strip those chars if they're there.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | sed 's/^\^D\x08\x08//' | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From ae768cc641c3b9ef370d22dd9c82c1f0bb7c22a9 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 08:44:13 -0500
Subject: [PATCH 28/44] testsuite, capturing intermediate files.

---
 tests/file_presentation.at | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/file_presentation.at b/tests/file_presentation.at
index 73127a69..100beb95 100644
--- a/tests/file_presentation.at
+++ b/tests/file_presentation.at
@@ -60,6 +60,8 @@ AT_DATA([test_file.cpp.expected],[test_file.cpp
 AT_CHECK([cat test_file.cpp.expected | $PROG_TOHEX > test_file.cpp.expected.hex], [0])
 
 AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
+AT_CAPTURE_FILE([test_file.cpp.expected.hex])
+AT_CAPTURE_FILE([stdout_tty])
 AT_CHECK([diff test_file.cpp.expected.hex stdout_tty], [0], [stdout], [stderr]) 
 
 

From 43ef9b04929401dedcb1369c919c7d9a6697abeb Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 08:55:24 -0500
Subject: [PATCH 29/44] Interim.

---
 configure.ac     |  5 +++--
 tests/atlocal.in | 11 ++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/configure.ac b/configure.ac
index 1f9256b0..6ca5e9eb 100644
--- a/configure.ac
+++ b/configure.ac
@@ -204,9 +204,10 @@ AC_PATH_PROG([PROG_PCRE2GREP], [pcre2grep], [])
 ###
 
 # Python, for generation of test suite.
-### @note Python >= 2.7 is actually required to run the testsuite at the moment, and hence is 
+### @note Python >= 2.7 is actually required to run the benchmarks in the testsuite at the moment, and hence is 
 ### not a maintainer-only tool.  My hope is that this will soon become a pre-"make distcheck" requirement.
-AM_PATH_PYTHON([2.7])
+AM_PATH_PYTHON([2.7],,[:])
+AM_CONDITIONAL([HAVE_PYTHON], [test "$PYTHON" != ":"])  #<< Automake conditional for skipping tests which require python.
 
 # Autotest needs autom4te, or 'missing's stub for it post-distribution. 
 AM_MISSING_PROG([AUTOM4TE], [autom4te])
diff --git a/tests/atlocal.in b/tests/atlocal.in
index 2c4e4103..ade17eb3 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -222,17 +222,18 @@ ASX_SCRIPT ()
 	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	#
-	# @note On some OSX systems (which detect as having a bsd-style 'script' utility), the below will prefix
-	#       the output with '^D<backspace><backspace>' (hex 5e  44  08  08).  Not clear why.  Until we figure that out, just
-	#       strip those chars if they're there.
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | sed 's/^\^D\x08\x08//' | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }
 
 # Pipe output through this to convert to an ASCII+Hex text representation.
 # Useful for detecting differences in non-printing characters. 
-PROG_TOHEX='od -t ax1'
+# @note On some OSX systems (which detect as having a bsd-style 'script' utility), tests such as this:
+#       AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
+#       will prefix stdout_tty with '^D<backspace><backspace>' (hex 5e  44  08  08).  Not clear why.  Until we figure that out, just
+#       strip those chars with sed if they're there.
+PROG_TOHEX='sed \'s/^\^D\x08\x08//\' | od -t ax1'
 

From 9f45bc78e5fd2fbbb41fa4ae78395d37e2d3c92a Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 09:04:28 -0500
Subject: [PATCH 30/44] Interim.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index ade17eb3..8489ec56 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -235,5 +235,5 @@ ASX_SCRIPT ()
 #       AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
 #       will prefix stdout_tty with '^D<backspace><backspace>' (hex 5e  44  08  08).  Not clear why.  Until we figure that out, just
 #       strip those chars with sed if they're there.
-PROG_TOHEX='sed \'s/^\^D\x08\x08//\' | od -t ax1'
+PROG_TOHEX='eval sed s/^\^D\x08\x08// | od -t ax1'
 

From 846d8bed79cefe950a4e86f391d192ffb31553a3 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 09:17:25 -0500
Subject: [PATCH 31/44] Interim.

---
 tests/file_presentation.at | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tests/file_presentation.at b/tests/file_presentation.at
index 100beb95..d71502ee 100644
--- a/tests/file_presentation.at
+++ b/tests/file_presentation.at
@@ -130,8 +130,13 @@ AT_DATA([expout],[@<:@32;1m@<:@Ktest_file.cpp@<:@0m@<:@K
 @<:@33;1m@<:@K3@<:@0m@<:@K:a@<:@30;43;1m@<:@Kbc@<:@0m@<:@Kd
 ])
 
+AT_CHECK([cat expout | $PROG_TOHEX > expout.hex], [0])
+AT_CAPTURE_FILE([expout.hex])
+
 # Check for color output to a TTY.
-AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --color 'bc'], [0], [expout])
+AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --color 'bc' | $PROG_TOHEX > stdout.hex], [0], [stdout], [stderr])
+AT_CAPTURE_FILE([stdout.hex])
+AT_CHECK([diff expout.hex stdout.hex], [0], [stdout], [stderr])
 
 # Check for nocolor to a TTY.
 AT_CHECK([ASX_SCRIPT ucg --noenv --cpp --nocolor 'bc'], [0], [test_file.cpp

From e2671133922d1119e43654207e331892c976875e Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 19:22:17 -0500
Subject: [PATCH 32/44] Interim.

---
 tests/atlocal.in | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 8489ec56..32ffe00a 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -223,8 +223,8 @@ ASX_SCRIPT ()
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	#
 	case $PROG_SCRIPT_TYPE in
-		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From b84c408036a4a1d09474e23b710343ad8b9b20c1 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 19:36:58 -0500
Subject: [PATCH 33/44] Interim.

---
 tests/file_presentation.at | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/file_presentation.at b/tests/file_presentation.at
index d71502ee..02aa6209 100644
--- a/tests/file_presentation.at
+++ b/tests/file_presentation.at
@@ -59,7 +59,7 @@ AT_DATA([test_file.cpp.expected],[test_file.cpp
 
 AT_CHECK([cat test_file.cpp.expected | $PROG_TOHEX > test_file.cpp.expected.hex], [0])
 
-AT_CHECK([{ ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ; } | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
+AT_CHECK([( ASX_SCRIPT ucg --noenv --cpp --nocolor --column 'do_something' ) | $PROG_TOHEX > stdout_tty], [0], [stdout], [stderr])
 AT_CAPTURE_FILE([test_file.cpp.expected.hex])
 AT_CAPTURE_FILE([stdout_tty])
 AT_CHECK([diff test_file.cpp.expected.hex stdout_tty], [0], [stdout], [stderr]) 

From 22277246cc3fde55678185db2b22950f3dc1c6b9 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 20:38:04 -0500
Subject: [PATCH 34/44] Interim.

---
 tests/atlocal.in | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 32ffe00a..831ff2c8 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -222,11 +222,14 @@ ASX_SCRIPT ()
 	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	#
+	original_stty_state=$(stty -g);
+	stty raw >/dev/null 2>&1;
 	case $PROG_SCRIPT_TYPE in
-		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
+	stty "$original_stty_state" >/dev/null 2>&1;
 }
 
 # Pipe output through this to convert to an ASCII+Hex text representation.

From 3c5298c5fee1cc39713712639ae3040026560be9 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 20:59:41 -0500
Subject: [PATCH 35/44] Interim.

---
 tests/atlocal.in | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 831ff2c8..859a6eda 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -222,14 +222,11 @@ ASX_SCRIPT ()
 	#         + /usr/bin/script -q /dev/null /bin/sh -c 'stty raw && ucg --noenv --cpp --nocolor --column do_something'
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	#
-	original_stty_state=$(stty -g);
-	stty raw >/dev/null 2>&1;
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT $SHELL -c "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
-	stty "$original_stty_state" >/dev/null 2>&1;
 }
 
 # Pipe output through this to convert to an ASCII+Hex text representation.

From 9d101fed1d0bb713ea0ee10ca75753cc9e465e89 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 21:07:11 -0500
Subject: [PATCH 36/44] Interim.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 859a6eda..d16e22e5 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -224,7 +224,7 @@ ASX_SCRIPT ()
 	#
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) echo $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From 91dece5c70f5b5c63b1e69a60693b12e6c758536 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 21:11:27 -0500
Subject: [PATCH 37/44] Interim.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index d16e22e5..87ed1fdc 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -224,7 +224,7 @@ ASX_SCRIPT ()
 	#
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) echo $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT exec "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From e8b0c739e78763a6ce11f226bce7bf40eac04d10 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Wed, 5 Oct 2016 21:29:24 -0500
Subject: [PATCH 38/44] Interim.

---
 tests/atlocal.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/atlocal.in b/tests/atlocal.in
index 87ed1fdc..15044236 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -224,7 +224,7 @@ ASX_SCRIPT ()
 	#
 	case $PROG_SCRIPT_TYPE in
 		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
-		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT exec "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT command eval "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac
 }

From d8a7047b2d766ccab09a13e74ef119431d298af8 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 02:51:14 -0500
Subject: [PATCH 39/44] Travis.

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 6c07689c..d3c89201 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,8 @@ matrix:
         - os: osx
           osx_image: xcode7.1
         - os: osx
-          osx_image: xcode8
+          osx_image: xcode7.3
+          #osx_image: xcode8
         - os: linux
           dist: trusty
           sudo: required

From 1792d0bcf5b5806265195080c9a2c2b875b7a259 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 03:04:31 -0500
Subject: [PATCH 40/44] Travis change to add pcre2 to linux builds.

---
 .travis.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d3c89201..eee2e958 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -27,8 +27,10 @@ before_install:
  # This is the recommended work-around until they fix it.
  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then brew uninstall libtool && brew install libtool; fi
  - if [ $TRAVIS_OS_NAME == osx ]; then brew install pcre pcre2 argp-standalone the_silver_searcher; fi
- - if [ $TRAVIS_OS_NAME == osx ]; then brew tap homebrew/dupes; brew install grep; fi  # Install gnu grep to test against. @todo Make things work so this can be installed only after a successful build.
+ # Install gnu grep to test against. @todo Make things work so this can be installed only after a successful build.
+ - if [ $TRAVIS_OS_NAME == osx ]; then brew tap homebrew/dupes; brew install grep; fi
  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq && sudo apt-get install -qq libpcre3-dev && sudo apt-get install -qq silversearcher-ag; fi
+ - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get install -qq libpcre2-dev; fi
 
 before_script:
  - echo "g++ --version:" && g++ --version && echo "===="

From 35301b415f67b0a679e9681d49e46c80bcbea5db Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 03:21:19 -0500
Subject: [PATCH 41/44] Put stty raw back for linux-style script.  Trying to
 get travis to pull down a pcre2 for trusty.

---
 .travis.yml      | 2 +-
 tests/atlocal.in | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index eee2e958..a94c0ee6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -30,7 +30,7 @@ before_install:
  # Install gnu grep to test against. @todo Make things work so this can be installed only after a successful build.
  - if [ $TRAVIS_OS_NAME == osx ]; then brew tap homebrew/dupes; brew install grep; fi
  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq && sudo apt-get install -qq libpcre3-dev && sudo apt-get install -qq silversearcher-ag; fi
- - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get install -qq libpcre2-dev; fi
+ - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get install -qq pcre2; fi
 
 before_script:
  - echo "g++ --version:" && g++ --version && echo "===="
diff --git a/tests/atlocal.in b/tests/atlocal.in
index 15044236..f50cc95b 100644
--- a/tests/atlocal.in
+++ b/tests/atlocal.in
@@ -223,7 +223,7 @@ ASX_SCRIPT ()
 	#       i.e. 'do_something' gets changed into an unquoted do_something.
 	#
 	case $PROG_SCRIPT_TYPE in
-		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "$(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
+		linux) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		bsd) $PROG_SCRIPT $PROG_SCRIPT_PRE_TEXT command eval "stty raw >/dev/null 2>&1 && $(printf '%s' "${*}")" $PROG_SCRIPT_POST_TEXT | tr -d '\r';;
 		*) exit 1;;
 	esac

From 469d4f8715b82f5d818dee6262942378e8f09258 Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 03:46:53 -0500
Subject: [PATCH 42/44] Removed OSX 10.11 from rotation due to stty issues from
 #103.

---
 .travis.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a94c0ee6..0bf6d525 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,9 +6,9 @@ matrix:
           osx_image: beta-xcode6.1
         - os: osx
           osx_image: xcode7.1
-        - os: osx
-          osx_image: xcode7.3
-          #osx_image: xcode8
+#        - os: osx # ==> OSX 10.11, 
+#          osx_image: xcode7.3
+#          osx_image: xcode8
         - os: linux
           dist: trusty
           sudo: required
@@ -30,7 +30,6 @@ before_install:
  # Install gnu grep to test against. @todo Make things work so this can be installed only after a successful build.
  - if [ $TRAVIS_OS_NAME == osx ]; then brew tap homebrew/dupes; brew install grep; fi
  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq && sudo apt-get install -qq libpcre3-dev && sudo apt-get install -qq silversearcher-ag; fi
- - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get install -qq pcre2; fi
 
 before_script:
  - echo "g++ --version:" && g++ --version && echo "===="

From 53a4ffa4c7fce44894253e70470854289f2adb2e Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 03:53:09 -0500
Subject: [PATCH 43/44] Comment on OSX 10.11.

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 0bf6d525..646385d3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ matrix:
           osx_image: beta-xcode6.1
         - os: osx
           osx_image: xcode7.1
-#        - os: osx # ==> OSX 10.11, 
+#        - os: osx # ==> OSX 10.11, removed until we have a fix for #103, tabs->spaces.
 #          osx_image: xcode7.3
 #          osx_image: xcode8
         - os: linux

From ba8636ac8ab8be128e525790a22bbaa9ec672cba Mon Sep 17 00:00:00 2001
From: "Gary R. Van Sickle" <grvs@users.sourceforge.net>
Date: Thu, 6 Oct 2016 04:02:23 -0500
Subject: [PATCH 44/44] Updated NEWS.md for issue #100.

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index fe0ec5c9..da47c698 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -32,7 +32,7 @@
 - Resolved issue with highlights on wrapped lines sometimes extending the full width of the terminal.  Resolves #80.
 - Resolved issue where matches spanning an eol (e.g. 'a\s+b' matching 'a\nb') would cause the program to throw an exception and terminate.  Resolves #92.
 - Resolved segfaults on some systems due to dirname() modifying its parameter.  Resolves #96.
-
+- No longer treating PCRE2 reporting no JIT support as an error.  Resolves #100.
 
 ## [0.2.2] - 2016-04-09