diff --git a/.gitignore b/.gitignore
index 19b18327..c6d4072f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -53,7 +53,7 @@ stamp-h1
 /yarac
 /libyara/modules/.dirstamp
 libyara/proc/.dirstamp
-libyara/yara.pc
+/yara.pc
 /tests/.dirstamp
 
 # Linux and Mac files
diff --git a/Makefile.am b/Makefile.am
index 95060970..2316169d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,11 +1,23 @@
-AM_CFLAGS=-Wall -I$(srcdir)/libyara/include
+ABI_VERSION = 9:0:1
+
+AM_CFLAGS=-Wall -D_GNU_SOURCE -I$(srcdir)/libyara/include
+
+#
+# When bison is used in POSIX yacc emulation mode (-y/--yacc option) it
+# produces warnings if we use Bison-specific features that are not supported
+# by yacc. With -Wno-yacc we turn off those warnings. Ideally we should call
+# bison without the -y/--yacc option, but autoconf insists on using bison in
+# yacc compatibility mode because of AC_PROG_YACC, and AC_PROG_BISON doesn't
+# exist.
+#
+AM_YFLAGS=-d -Wno-yacc
 
 if GCOV
 
 check:
 	@tests/gcov-summary
 
-MOSTLYCLEANFILES = {cli,tests}/*.gc{no,da,ov}
+MOSTLYCLEANFILES = {cli,tests,libyara,libyara/proc,libyara/modules/*}/*.gc{no,da,ov}
 AM_CFLAGS+=-O0 -g -ftest-coverage -fprofile-arcs
 
 else
@@ -30,12 +42,221 @@ if UB_SANITIZER
 AM_CFLAGS+=-fsanitize=undefined -fno-sanitize-recover=undefined
 endif
 
-# Build the library in the hand subdirectory first.
-SUBDIRS = libyara
-DIST_SUBDIRS = libyara
-
 ACLOCAL_AMFLAGS=-I m4
 
+# Rules for generating YARA modules from .proto files. For each .proto file
+# three files are generated: .c, .pb-c.c, and .pb-c.h. The .c file is generated
+# by protoc-gen-yara and the other two by protoc-gen-c. This is done only if
+# protoc is found, if not, files already in the repository are used instead
+# of generating fresh ones from the .proto file.
+#
+if PROTOC
+# SUFFIXES = .proto .pb-c.c .pb-c.h .c
+.proto.pb-c.c:
+		$(PROTOC) --c_out=$(builddir) $^ -Ilibyara/pb/ -I=$(srcdir)
+
+.proto.pb-c.h:
+		$(PROTOC) --c_out=$(builddir) $^ -Ilibyara/pb/ -I=$(srcdir)
+
+.proto.c:
+		$(PROTOC) --c_out=$(builddir) $^ -Ilibyara/pb/ -I=$(srcdir)
+endif
+
+MODULES =  libyara/modules/tests/tests.c
+
+MODULES += libyara/modules/elf/elf.c
+
+MODULES += libyara/modules/math/math.c
+
+MODULES += libyara/modules/time/time.c
+
+MODULES += libyara/modules/pe/pe.c
+MODULES += libyara/modules/pe/pe_utils.c
+
+MODULES += libyara/modules/console/console.c
+
+MODULES += libyara/modules/string/string.c
+
+if CUCKOO_MODULE
+MODULES += libyara/modules/cuckoo/cuckoo.c
+endif
+
+if MAGIC_MODULE
+MODULES += libyara/modules/magic/magic.c
+endif
+
+if HASH_MODULE
+MODULES += libyara/modules/hash/hash.c
+endif
+
+if DOTNET_MODULE
+MODULES += libyara/modules/dotnet/dotnet.c
+endif
+
+if MACHO_MODULE
+MODULES += libyara/modules/macho/macho.c
+endif
+
+if DEX_MODULE
+MODULES += libyara/modules/dex/dex.c
+endif
+
+if PB_TESTS_MODULE
+MODULES += libyara/modules/pb_tests/pb_tests.c
+MODULES += libyara/modules/pb_tests/pb_tests.pb-c.c
+endif
+
+if AUTHENTICODE_MODULE
+MODULES += libyara/modules/pe/authenticode-parser/authenticode.c
+MODULES += libyara/modules/pe/authenticode-parser/certificate.c
+MODULES += libyara/modules/pe/authenticode-parser/helper.c
+MODULES += libyara/modules/pe/authenticode-parser/countersignature.c
+MODULES += libyara/modules/pe/authenticode-parser/structs.c
+endif
+
+#
+# Add your modules here:
+#
+# MODULES += libyara/modules/yourmodule.c
+#
+
+include_HEADERS = libyara/include/yara.h
+
+yaraincludedir = $(includedir)/yara
+yarainclude_HEADERS = \
+	libyara/include/yara/ahocorasick.h \
+	libyara/include/yara/arena.h \
+	libyara/include/yara/atoms.h \
+	libyara/include/yara/base64.h \
+	libyara/include/yara/bitmask.h \
+	libyara/include/yara/compiler.h \
+	libyara/include/yara/error.h \
+	libyara/include/yara/exec.h \
+	libyara/include/yara/exefiles.h \
+	libyara/include/yara/filemap.h \
+	libyara/include/yara/hash.h \
+	libyara/include/yara/integers.h \
+	libyara/include/yara/libyara.h \
+	libyara/include/yara/limits.h \
+	libyara/include/yara/mem.h \
+	libyara/include/yara/modules.h \
+	libyara/include/yara/notebook.h \
+	libyara/include/yara/object.h \
+	libyara/include/yara/parser.h \
+	libyara/include/yara/proc.h \
+	libyara/include/yara/re.h \
+	libyara/include/yara/rules.h \
+	libyara/include/yara/scan.h \
+	libyara/include/yara/scanner.h \
+	libyara/include/yara/simple_str.h \
+	libyara/include/yara/sizedstr.h \
+	libyara/include/yara/stack.h \
+	libyara/include/yara/stopwatch.h \
+	libyara/include/yara/stream.h \
+	libyara/include/yara/strutils.h \
+	libyara/include/yara/threading.h \
+	libyara/include/yara/types.h \
+	libyara/include/yara/unaligned.h \
+	libyara/include/yara/utils.h
+
+noinst_HEADERS = \
+	libyara/crypto.h \
+	libyara/exception.h \
+	libyara/include/yara/dotnet.h \
+	libyara/include/yara/elf.h \
+	libyara/include/yara/endian.h \
+	libyara/include/yara/globals.h \
+	libyara/include/yara/hex_lexer.h \
+	libyara/include/yara/lexer.h \
+	libyara/include/yara/pe.h \
+	libyara/include/yara/pe_utils.h \
+	libyara/include/yara/re_lexer.h \
+	libyara/modules/module_list
+
+dist_noinst_DATA = libyara/pb/yara.proto
+
+lib_LTLIBRARIES = libyara.la
+
+libyara_la_CFLAGS = $(AM_CFLAGS) -I$(srcdir)/libyara
+libyara_la_LDFLAGS = -version-number $(ABI_VERSION)
+
+BUILT_SOURCES = \
+	libyara/lexer.c \
+	libyara/hex_lexer.c \
+	libyara/re_lexer.c \
+	libyara/grammar.c libyara/grammar.h \
+	libyara/hex_grammar.c libyara/hex_grammar.h \
+	libyara/re_grammar.c libyara/re_grammar.h
+
+libyara_la_SOURCES = \
+	$(MODULES) \
+	libyara/grammar.y \
+	libyara/ahocorasick.c \
+	libyara/arena.c \
+	libyara/atoms.c \
+	libyara/base64.c \
+	libyara/bitmask.c \
+	libyara/compiler.c \
+	libyara/endian.c \
+	libyara/exec.c \
+	libyara/exefiles.c \
+	libyara/filemap.c \
+	libyara/hash.c \
+	libyara/hex_grammar.y \
+	libyara/hex_lexer.l \
+	libyara/lexer.l \
+	libyara/libyara.c \
+	libyara/mem.c \
+	libyara/modules.c \
+	libyara/notebook.c \
+	libyara/object.c \
+	libyara/parser.c \
+	libyara/proc.c \
+	libyara/re.c \
+	libyara/re_grammar.y \
+	libyara/re_lexer.l \
+	libyara/rules.c \
+	libyara/scan.c \
+	libyara/scanner.c \
+	libyara/simple_str.c \
+	libyara/sizedstr.c \
+	libyara/stack.c \
+	libyara/stopwatch.c \
+	libyara/strutils.c \
+	libyara/stream.c \
+	libyara/tlshc/tlsh.c \
+	libyara/tlshc/tlsh_impl.c \
+	libyara/tlshc/tlsh_util.c \
+	libyara/threading.c
+
+
+if USE_WINDOWS_PROC
+libyara_la_SOURCES += libyara/proc/windows.c
+endif
+
+if USE_LINUX_PROC
+libyara_la_SOURCES += libyara/proc/linux.c
+endif
+
+if USE_FREEBSD_PROC
+libyara_la_SOURCES += libyara/proc/freebsd.c
+endif
+
+if USE_OPENBSD_PROC
+libyara_la_SOURCES += libyara/proc/openbsd.c
+endif
+
+if USE_MACH_PROC
+libyara_la_SOURCES += libyara/proc/mach.c
+endif
+
+if USE_NO_PROC
+libyara_la_SOURCES += libyara/proc/none.c
+endif
+
+pkgconfigdir = $(libdir)/pkgconfig
+nodist_pkgconfig_DATA = yara.pc
+
 bin_PROGRAMS = yara yarac
 
 yara_SOURCES = \
@@ -47,8 +268,7 @@ yara_SOURCES = \
   cli/threading.h \
   cli/yara.c
 
-yara_LDADD = -Llibyara/.libs -lyara
-yara_DEPENDENCIES = libyara/.libs/libyara.la
+yara_LDADD = libyara.la
 
 yarac_SOURCES = \
    cli/args.c \
@@ -57,43 +277,42 @@ yarac_SOURCES = \
    cli/common.h \
    cli/yarac.c
 
-yarac_LDADD = -Llibyara/.libs -lyara
-yarac_DEPENDENCIES = libyara/.libs/libyara.la
+yarac_LDADD = libyara.la
 
 tests_mapper_SOURCES = tests/mapper.c
 tests_mapper_CFLAGS = -O0
 
 test_alignment_SOURCES = tests/test-alignment.c tests/util.c
-test_alignment_LDADD = libyara/.libs/libyara.a
+test_alignment_LDADD = libyara.la
 test_arena_SOURCES = tests/test-arena.c tests/util.c
-test_arena_LDADD = libyara/.libs/libyara.a
+test_arena_LDADD = libyara.la
 test_atoms_SOURCES = tests/test-atoms.c tests/util.c
-test_atoms_LDADD = libyara/.libs/libyara.a
+test_atoms_LDADD = libyara.la
 test_rules_SOURCES = tests/test-rules.c tests/util.c
-test_rules_LDADD = libyara/.libs/libyara.a
+test_rules_LDADD = libyara.la
 if POSIX
 EXTRA_test_rules_DEPENDENCIES = tests/mapper$(EXEEXT)
 endif
 test_pe_SOURCES = tests/test-pe.c tests/util.c
-test_pe_LDADD = libyara/.libs/libyara.a
+test_pe_LDADD = libyara.la
 test_elf_SOURCES = tests/test-elf.c tests/util.c
-test_elf_LDADD = libyara/.libs/libyara.a
+test_elf_LDADD = libyara.la
 test_version_SOURCES = tests/test-version.c tests/util.c
-test_version_LDADD = libyara/.libs/libyara.a
+test_version_LDADD = libyara.la
 test_api_SOURCES = tests/test-api.c tests/util.c
-test_api_LDADD = libyara/.libs/libyara.a
+test_api_LDADD = libyara.la
 test_bitmask_SOURCES = tests/test-bitmask.c tests/util.c
-test_bitmask_LDADD = libyara/.libs/libyara.a
+test_bitmask_LDADD = libyara.la
 test_math_SOURCES = tests/test-math.c tests/util.c
-test_math_LDADD = libyara/.libs/libyara.a
+test_math_LDADD = libyara.la
 test_string_SOURCES = tests/test-string.c tests/util.c
-test_string_LDADD = libyara/.libs/libyara.a
+test_string_LDADD = libyara.la
 test_stack_SOURCES = tests/test-stack.c tests/util.c
-test_stack_LDADD = libyara/.libs/libyara.a
+test_stack_LDADD = libyara.la
 test_re_split_SOURCES = tests/test-re-split.c tests/util.c
-test_re_split_LDADD = libyara/.libs/libyara.a
+test_re_split_LDADD = libyara.la
 test_async_SOURCES = tests/test-async.c tests/util.c
-test_async_LDADD = libyara/.libs/libyara.a
+test_async_LDADD = libyara.la
 
 TESTS = $(check_PROGRAMS)
 TESTS_ENVIRONMENT = TOP_SRCDIR=$(top_srcdir) TOP_BUILDDIR=$(top_builddir)
@@ -123,38 +342,38 @@ if POSIX
 if !ADDRESS_SANITIZER
 check_PROGRAMS+=test-exception
 test_exception_SOURCES = tests/test-exception.c tests/util.c
-test_exception_LDADD = libyara/.libs/libyara.a
+test_exception_LDADD = libyara.la
 endif
 endif
 
 if MACHO_MODULE
 check_PROGRAMS+=test-macho
 test_macho_SOURCES = tests/test-macho.c tests/util.c
-test_macho_LDADD = libyara/.libs/libyara.a
+test_macho_LDADD = libyara.la
 endif
 
 if DEX_MODULE
 check_PROGRAMS+=test-dex
 test_dex_SOURCES = tests/test-dex.c tests/util.c
-test_dex_LDADD = libyara/.libs/libyara.a
+test_dex_LDADD = libyara.la
 endif
 
 if DOTNET_MODULE
 check_PROGRAMS+=test-dotnet
 test_dotnet_SOURCES = tests/test-dotnet.c tests/util.c
-test_dotnet_LDADD = libyara/.libs/libyara.a
+test_dotnet_LDADD = libyara.la
 endif
 
 if MAGIC_MODULE
 check_PROGRAMS+=test-magic
 test_magic_SOURCES = tests/test-magic.c tests/util.c
-test_magic_LDADD = libyara/.libs/libyara.a
+test_magic_LDADD = libyara.la
 endif
 
 if PB_TESTS_MODULE
 check_PROGRAMS+=test-pb
 test_pb_SOURCES = tests/test-pb.c tests/util.c
-test_pb_LDADD = libyara/.libs/libyara.a
+test_pb_LDADD = libyara.la
 endif
 
 # man pages
diff --git a/configure.ac b/configure.ac
index 9394233b..392baa64 100644
--- a/configure.ac
+++ b/configure.ac
@@ -376,7 +376,6 @@ AC_SUBST([PC_REQUIRES_PRIVATE])
 AC_SUBST([PC_LIBS_PRIVATE])
 
 AC_CONFIG_FILES([Makefile])
-AC_CONFIG_FILES([libyara/Makefile])
-AC_CONFIG_FILES([libyara/yara.pc])
+AC_CONFIG_FILES([yara.pc])
 
 AC_OUTPUT
diff --git a/libyara/Makefile.am b/libyara/Makefile.am
deleted file mode 100644
index a608913f..00000000
--- a/libyara/Makefile.am
+++ /dev/null
@@ -1,277 +0,0 @@
-# ABI_VERSION is passed to libtool as --version-number $(ABI_VERSION). This is
-# not related to YARA's release version, this is used for tracking changes in
-# the ABI, not in the project as a whole.
-#
-# The three number mean [current]:[revision]:[age], and they should updated as
-# follow:
-#
-# 1. With every release increment "revision".
-#
-# 2. If any interfaces have been added, removed, or changed since the last
-#    update, increment "current" and set "revision" to 0.
-#
-# 3. If the changes in the interface were backward compatible (i.e: only adding
-#    new APIs) increment "age", or set it to 0 if otherwise.
-#
-# See https://autotools.io/libtool/version.html for more details.
-#
-ABI_VERSION = 9:0:1
-
-# Rules for generating YARA modules from .proto files. For each .proto file
-# three files are generated: .c, .pb-c.c, and .pb-c.h. The .c file is generated
-# by protoc-gen-yara and the other two by protoc-gen-c. This is done only if
-# protoc is found, if not, files already in the repository are used instead
-# of generating fresh ones from the .proto file.
-#
-if PROTOC
-SUFFIXES = .proto .pb-c.c .pb-c.h .c
-.proto.pb-c.c:
-		$(PROTOC) --c_out=$(builddir) $^ -Ipb/ -I=$(srcdir)
-
-.proto.pb-c.h:
-		$(PROTOC) --c_out=$(builddir) $^ -Ipb/ -I=$(srcdir)
-
-.proto.c:
-		$(PROTOC) --c_out=$(builddir) $^ -Ipb/ -I=$(srcdir)
-endif
-
-MODULES =  modules/tests/tests.c
-
-MODULES += modules/elf/elf.c
-
-MODULES += modules/math/math.c
-
-MODULES += modules/time/time.c
-
-MODULES += modules/pe/pe.c
-MODULES += modules/pe/pe_utils.c
-
-MODULES += modules/console/console.c
-
-MODULES += modules/string/string.c
-
-if CUCKOO_MODULE
-MODULES += modules/cuckoo/cuckoo.c
-endif
-
-if MAGIC_MODULE
-MODULES += modules/magic/magic.c
-endif
-
-if HASH_MODULE
-MODULES += modules/hash/hash.c
-endif
-
-if DOTNET_MODULE
-MODULES += modules/dotnet/dotnet.c
-endif
-
-if MACHO_MODULE
-MODULES += modules/macho/macho.c
-endif
-
-if DEX_MODULE
-MODULES += modules/dex/dex.c
-endif
-
-if PB_TESTS_MODULE
-MODULES += modules/pb_tests/pb_tests.c
-MODULES += modules/pb_tests/pb_tests.pb-c.c
-endif
-
-if AUTHENTICODE_MODULE
-MODULES += modules/pe/authenticode-parser/authenticode.c
-MODULES += modules/pe/authenticode-parser/certificate.c
-MODULES += modules/pe/authenticode-parser/helper.c
-MODULES += modules/pe/authenticode-parser/countersignature.c
-MODULES += modules/pe/authenticode-parser/structs.c
-endif
-
-#
-# Add your modules here:
-#
-# MODULES += modules/yourmodule.c
-#
-
-#
-# When bison is used in POSIX yacc emulation mode (-y/--yacc option) it
-# produces warnings if we use Bison-specific features that are not supported
-# by yacc. With -Wno-yacc we turn off those warnings. Ideally we should call
-# bison without the -y/--yacc option, but autoconf insists on using bison in
-# yacc compatibility mode because of AC_PROG_YACC, and AC_PROG_BISON doesn't
-# exist.
-#
-AM_YFLAGS=-d -Wno-yacc
-
-AM_CFLAGS=-Wall -Wno-deprecated-declarations \
-	-D_GNU_SOURCE \
-	-I$(srcdir)/include
-
-if GCOV
-MOSTLYCLEANFILES = {.,proc,modules/*}/*.gc{no,da,ov}
-AM_CFLAGS+=-O0 -g -ftest-coverage -fprofile-arcs
-else
-
-if DEBUG
-AM_CFLAGS+=-g
-endif
-
-if OPTIMIZATION
-AM_CFLAGS+=-O3
-else
-AM_CFLAGS+=-O0
-endif
-
-endif
-
-
-if ADDRESS_SANITIZER
-AM_CFLAGS+=-fsanitize=address
-endif
-
-if UB_SANITIZER
-AM_CFLAGS+=-fsanitize=undefined -fno-sanitize-recover=undefined
-endif
-
-if GCC
-AM_CFLAGS+=-fvisibility=hidden
-endif
-
-ACLOCAL_AMFLAGS=-I m4
-
-include_HEADERS = include/yara.h
-
-yaraincludedir = $(includedir)/yara
-yarainclude_HEADERS = \
-	include/yara/ahocorasick.h \
-	include/yara/arena.h \
-	include/yara/atoms.h \
-	include/yara/base64.h \
-	include/yara/bitmask.h \
-	include/yara/compiler.h \
-	include/yara/error.h \
-	include/yara/exec.h \
-	include/yara/exefiles.h \
-	include/yara/filemap.h \
-	include/yara/hash.h \
-	include/yara/integers.h \
-	include/yara/libyara.h \
-	include/yara/limits.h \
-	include/yara/mem.h \
-	include/yara/modules.h \
-	include/yara/notebook.h \
-	include/yara/object.h \
-	include/yara/parser.h \
-	include/yara/proc.h \
-	include/yara/re.h \
-	include/yara/rules.h \
-	include/yara/scan.h \
-	include/yara/scanner.h \
-	include/yara/simple_str.h \
-	include/yara/sizedstr.h \
-	include/yara/stack.h \
-	include/yara/stopwatch.h \
-	include/yara/stream.h \
-	include/yara/strutils.h \
-	include/yara/threading.h \
-	include/yara/types.h \
-	include/yara/unaligned.h \
-	include/yara/utils.h
-
-noinst_HEADERS = \
-	crypto.h \
-	exception.h \
-	include/yara/dotnet.h \
-	include/yara/elf.h \
-	include/yara/endian.h \
-	include/yara/globals.h \
-	include/yara/hex_lexer.h \
-	include/yara/lexer.h \
-	include/yara/pe.h \
-	include/yara/pe_utils.h \
-	include/yara/re_lexer.h \
-	modules/module_list
-
-dist_noinst_DATA = pb/yara.proto
-
-
-lib_LTLIBRARIES = libyara.la
-
-libyara_la_LDFLAGS = -version-number $(ABI_VERSION)
-
-BUILT_SOURCES = \
-	lexer.c \
-	hex_lexer.c \
-	re_lexer.c \
-	grammar.c \
-	hex_grammar.c \
-	re_grammar.c
-
-libyara_la_SOURCES = \
-	$(MODULES) \
-	grammar.y \
-	ahocorasick.c \
-	arena.c \
-	atoms.c \
-	base64.c \
-	bitmask.c \
-	compiler.c \
-	endian.c \
-	exec.c \
-	exefiles.c \
-	filemap.c \
-	hash.c \
-	hex_grammar.y \
-	hex_lexer.l \
-	lexer.l \
-	libyara.c \
-	mem.c \
-	modules.c \
-	notebook.c \
-	object.c \
-	parser.c \
-	proc.c \
-	re.c \
-	re_grammar.y \
-	re_lexer.l \
-	rules.c \
-	scan.c \
-	scanner.c \
-	simple_str.c \
-	sizedstr.c \
-	stack.c \
-	stopwatch.c \
-	strutils.c \
-	stream.c \
-	tlshc/tlsh.c \
-	tlshc/tlsh_impl.c \
-	tlshc/tlsh_util.c \
-	threading.c
-
-
-if USE_WINDOWS_PROC
-libyara_la_SOURCES += proc/windows.c
-endif
-
-if USE_LINUX_PROC
-libyara_la_SOURCES += proc/linux.c
-endif
-
-if USE_FREEBSD_PROC
-libyara_la_SOURCES += proc/freebsd.c
-endif
-
-if USE_OPENBSD_PROC
-libyara_la_SOURCES += proc/openbsd.c
-endif
-
-if USE_MACH_PROC
-libyara_la_SOURCES += proc/mach.c
-endif
-
-if USE_NO_PROC
-libyara_la_SOURCES += proc/none.c
-endif
-
-pkgconfigdir = $(libdir)/pkgconfig
-nodist_pkgconfig_DATA = yara.pc
diff --git a/libyara/yara.pc.in b/yara.pc.in
similarity index 100%
rename from libyara/yara.pc.in
rename to yara.pc.in