IMHO, the build system could do with a little work:

* The various bits generated from and added by the autotools shouldn't be committed. autoreconf -i works really well these days. That's INSTALL Makefile.in aclocal.m4 compile config.guess config.h.in config.sub configure depcomp install-sh ltmain.sh missing mkinstalldirs.

configure.ac:

* Needs to call AC_SUBST([LIBTOOL_DEPS]) or else the rule to rebuild libtool in Makefile.am won't work.

* A lot of macro calls are underquoted. It'll probably work fine, but it's poor style.

* The dance with EXTRA_LIBSNAPPY_LDFLAGS seems odd. It'd be more conventional to do something like:

SNAPPY_LTVERSION=snappy_version
AC_SUBST([SNAPPY_LTVERSION])

and set the -version-info flag directly in Makefile.am. If it's to allow the user to provide custom LDFLAGS, it's unnecessary: LDFLAGS is part of libsnappy_la_LINK. Here's the snippet from Makefile.in:

libsnappy_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
$(CXXFLAGS) $(libsnappy_la_LDFLAGS) $(LDFLAGS) -o $@

* There should be an AC_ARG_WITH for gflags, because automagic dependencies aren't cool: http://www.gentoo.org/proj/en/qa/automagic.xml

* Shell variables starting with ac_ are in autoconf's namespace. Setting things like ac_have_builtin_ctz is therefore equally uncool. See http://www.gnu.org/s/hello/manual/autoconf/Macro-Names.html :

> To ensure that your macros don't conflict with present or future Autoconf macros, you should prefix your own macro names and any shell variables they use with some other sequence. Possibilities include your initials, or an abbreviation for the name of your organization or software package.

* Use AS_IF instead of directly using the shell's `if`: http://www.gnu.org/software/hello/manual/autoconf/Limitation... and http://www.gnu.org/s/hello/manual/autoconf/Common-Shell-Cons... .

* Consider adding -Wall to either AUTOMAKE_OPTIONS in Makefile.am or as an argument to AM_INIT_AUTOMAKE. If you don't mind using a modern automake (1.11 or later), also call AM_SILENT_RULES([yes]). Even MSYS has automake-1.11 these days.

Makefile.am:

* Adding $(GTEST_CPPFLAGS) to both snappy_unittest_CPPFLAGS and snappy_unittest_CXXFLAGS is redundant. See this part of Makefile.in:

snappy_unittest-snappy-test.o: snappy-test.cc
@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(snappy_unittest_CPPFLAGS) $(CPPFLAGS) $(snappy_unittest_CXXFLAGS) $(CXXFLAGS) -MT snappy_unittest-snappy-test.o -MD -MP -MF $(DEPDIR)/snappy_unittest-snappy-test.Tpo -c -o snappy_unittest-snappy-test.o `test -f 'snappy-test.cc' || echo '$(srcdir)/'`snappy-test.cc
@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/snappy_unittest-snappy-test.Tpo $(DEPDIR)/snappy_unittest-snappy-test.Po
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='snappy-test.cc' object='snappy_unittest-snappy-test.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(snappy_unittest_CPPFLAGS) $(CPPFLAGS) $(snappy_unittest_CXXFLAGS) $(CXXFLAGS) -c -o snappy_unittest-snappy-test.o `test -f 'snappy-test.cc' || echo '$(srcdir)/'`snappy-test.cc

* snappy_unittest should be in check_PROGRAMS, not noinst_PROGRAMS. That way, it's built as part of `make check`, not `make all`.