diff --git a/Makefile b/Makefile
index bc3ccb02..fbd087c7 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 -include config.mk
 
-SUBDIRS	= include lib bin etc data
+SUBDIRS	= include lib bin data
 
 ifdef BUILD_API_DOCS
 SUBDIRS += doc
diff --git a/NEWS b/NEWS
index 0843c459..96837e73 100644
--- a/NEWS
+++ b/NEWS
@@ -1,5 +1,24 @@
 xbps-0.42 (???):
 
+ * utils: the -C/--config option now expects a path to a directory storing
+   configuration files; if first character is not '/' it will be treated as
+   relative to rootdir.
+
+ * <sysconfdir>/xbps/xbps.conf is not longer installed, in fact there are no files
+   installed anymore to sysconfdir. The xbps.conf file with everything commented out
+   is now installed to <sharedir>/xbps.d/xbps.conf just as example.
+
+ * Replaced config/system {preserve,repo,virtualpkg}.d directories with a single
+   xbps.d directory that may contain configuration files of all kinds:
+   general options, repositories, virtual packages, and preserved files.
+   By default set to <sysconfdir>/xbps.d and <sharedir>/xbps.d:
+
+	- /usr/local/etc/xbps.d 	<- configuration directory
+	- /usr/local/share/xbps.d	<- system configuration directory
+
+   Files bearing the same filename in the configuration directory override
+   those available in the system configuration directory.
+
  * Virtual packages are now collected directly from pkgdb, that means
    that installed packages do not need to have a virtualpkg configuration
    file in the system virtualpkg.d directory.
diff --git a/bin/xbps-checkvers/main.c b/bin/xbps-checkvers/main.c
index 4d0609bd..2ff38bac 100644
--- a/bin/xbps-checkvers/main.c
+++ b/bin/xbps-checkvers/main.c
@@ -211,12 +211,10 @@ rcv_init(rcv_t *rcv, const char *prog)
 	rcv->have_vars = 0;
 	rcv->ptr = rcv->input = NULL;
 	if (rcv->xbps_conf != NULL) {
-		strncpy(rcv->xhp.conffile, rcv->xbps_conf, sizeof(rcv->xhp.conffile)-1);
-		rcv->xhp.conffile[sizeof(rcv->xhp.conffile)-1] = '\0';
+		xbps_strlcpy(rcv->xhp.confdir, rcv->xbps_conf, sizeof(rcv->xhp.confdir));
 	}
 	if (rcv->rootdir != NULL) {
-		strncpy(rcv->xhp.rootdir, rcv->rootdir, sizeof(rcv->xhp.rootdir)-1);
-		rcv->xhp.rootdir[sizeof(rcv->xhp.rootdir)-1] = '\0';
+		xbps_strlcpy(rcv->xhp.rootdir, rcv->rootdir, sizeof(rcv->xhp.rootdir));
 	}
 	if (xbps_init(&rcv->xhp) != 0)
 		abort();
@@ -507,11 +505,12 @@ rcv_find_conf(rcv_t *rcv)
 }
 
 static bool
-check_reverts(const char *repover, const map_item_t reverts) {
+check_reverts(const char *repover, const map_item_t reverts)
+{
 	bool rv = false;
 	char *sreverts, *p;
 
-	if(reverts.v.len == 0)
+	if (reverts.v.len == 0)
 		return rv;
 
 	sreverts = calloc(reverts.v.len+1, sizeof(char));
@@ -523,14 +522,14 @@ check_reverts(const char *repover, const map_item_t reverts) {
 		 * Check if it's the first character or the previous character is a
 		 * whitespace.
 		 */
-		if(p > sreverts && !isspace(p[-1]))
+		if (p > sreverts && !isspace(p[-1]))
 			continue;
 		p += strlen(repover);
 		/*
 		 * Check if it's the last character or if the next character is a
 		 * whitespace
 		 */
-		if(isspace(*p) || *p == '\0') {
+		if (isspace(*p) || *p == '\0') {
 			rv = true;
 			break;
 		}
diff --git a/bin/xbps-checkvers/xbps-checkvers.8 b/bin/xbps-checkvers/xbps-checkvers.8
index 613428fd..e97a0b73 100644
--- a/bin/xbps-checkvers/xbps-checkvers.8
+++ b/bin/xbps-checkvers/xbps-checkvers.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-CHECKVERS 8
 .Sh NAME
 .Nm xbps-checkvers
@@ -24,8 +24,10 @@ tree. The
 argument sets extra packages to process with the outdated ones (only processed if missing).
 .Sh OPTIONS
 .Bl -tag -width -x
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl D, Fl -distdir Ar dir
 Specifies a full path to the void-packages repository. By default set to
 .Nm ~/void-packages .
diff --git a/bin/xbps-dgraph/main.c b/bin/xbps-dgraph/main.c
index 1b1c991a..a16db482 100644
--- a/bin/xbps-dgraph/main.c
+++ b/bin/xbps-dgraph/main.c
@@ -480,7 +480,7 @@ main(int argc, char **argv)
 	/* Initialize libxbps */
 	memset(&xh, 0, sizeof(xh));
 	if (rootdir != NULL)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
 
 	if ((rv = xbps_init(&xh)) != 0)
 		die("failed to initialize libxbps: %s", strerror(rv));
diff --git a/bin/xbps-install/main.c b/bin/xbps-install/main.c
index 6169faec..1921ade5 100644
--- a/bin/xbps-install/main.c
+++ b/bin/xbps-install/main.c
@@ -44,8 +44,8 @@ usage(bool fail)
 	    "Usage: xbps-install [OPTIONS] [PKGNAME...]\n\n"
 	    "OPTIONS\n"
 	    " -A --automatic           Set automatic installation mode\n"
-	    " -C --config <file>       Full path to configuration file\n"
-	    " -c --cachedir <dir>      Full path to cachedir\n"
+	    " -C --config <dir>        Path to confdir (xbps.d)\n"
+	    " -c --cachedir <dir>      Path to cachedir\n"
 	    " -d --debug               Debug mode shown to stderr\n"
 	    " -f --force               Force package re-installation\n"
 	    "                          If specified twice, all files will be\n"
@@ -110,12 +110,12 @@ main(int argc, char **argv)
 	};
 	struct xbps_handle xh;
 	struct xferstat xfer;
-	const char *rootdir, *cachedir, *conffile;
+	const char *rootdir, *cachedir, *confdir;
 	int i, c, flags, rv, fflag = 0;
 	bool syncf, yes, reinstall, drun, update;
 	int maxcols;
 
-	rootdir = cachedir = conffile = NULL;
+	rootdir = cachedir = confdir = NULL;
 	flags = rv = 0;
 	syncf = yes = reinstall = drun = update = false;
 
@@ -127,7 +127,7 @@ main(int argc, char **argv)
 			flags |= XBPS_FLAG_INSTALL_AUTO;
 			break;
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'c':
 			cachedir = optarg;
@@ -187,11 +187,11 @@ main(int argc, char **argv)
 	xh.fetch_cb = fetch_file_progress_cb;
 	xh.fetch_cb_data = &xfer;
 	if (rootdir)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
 	if (cachedir)
-		strncpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
-	if (conffile)
-		strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+		xbps_strlcpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
+	if (confdir)
+		xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 	xh.flags = flags;
 	if (flags & XBPS_FLAG_VERBOSE)
 		xh.unpack_cb = unpack_progress_cb;
diff --git a/bin/xbps-install/xbps-install.8 b/bin/xbps-install/xbps-install.8
index d02de7ca..42cd7975 100644
--- a/bin/xbps-install/xbps-install.8
+++ b/bin/xbps-install/xbps-install.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-INSTALL 8
 .Sh NAME
 .Nm xbps-install
@@ -59,10 +59,14 @@ The first repository matching the package expression wins.
 .It Fl A, Fl -automatic
 Enables automatic installation mode, i.e. package will be treated as orphan
 if no package is depending on it directly.
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl c, Fl -cachedir Ar dir
-Specifies a full path to the cache directory, where binary packages are stored.
+Specifies a path to the cache directory, where binary packages are stored.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl d, Fl -debug
 Enables extra debugging shown to stderr.
 .It Fl f, Fl -force
@@ -111,8 +115,8 @@ the native architecture).
 .El
 .Sh FILES
 .Bl -tag -width /var/db/xbps/.<pkgname>-files.plist
-.It Ar /etc/xbps/xbps.conf
-Default configuration file.
+.It Ar /etc/xbps.d
+Default configuration directory.
 .It Ar /var/db/xbps/.<pkgname>-files.plist
 Package files metadata.
 .It Ar /var/db/xbps/pkgdb-0.38.plist
diff --git a/bin/xbps-pkgdb/main.c b/bin/xbps-pkgdb/main.c
index f1b67e9d..f21d7b1e 100644
--- a/bin/xbps-pkgdb/main.c
+++ b/bin/xbps-pkgdb/main.c
@@ -41,7 +41,7 @@ usage(bool fail)
 	    "Usage: xbps-pkgdb [OPTIONS] [PKGNAME...]\n\n"
 	    "OPTIONS\n"
 	    " -a --all                               Process all packages\n"
-	    " -C --config <file>                     Full path to configuration file\n"
+	    " -C --config <dir>                      Path to confdir (xbps.d)\n"
 	    " -d --debug                             Debug mode shown to stderr\n"
 	    " -h --help                              Print usage help\n"
 	    " -m --mode <auto|manual|hold|unhold>    Change PKGNAME to this mode\n"
@@ -92,7 +92,7 @@ main(int argc, char **argv)
 		{ NULL, 0, NULL, 0 }
 	};
 	struct xbps_handle xh;
-	const char *conffile = NULL, *rootdir = NULL, *instmode = NULL;
+	const char *confdir = NULL, *rootdir = NULL, *instmode = NULL;
 	int c, i, rv, flags = 0;
 	bool update_format = false, all = false;
 
@@ -102,7 +102,7 @@ main(int argc, char **argv)
 			all = true;
 			break;
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'd':
 			flags |= XBPS_FLAG_DEBUG;
@@ -136,9 +136,9 @@ main(int argc, char **argv)
 
 	memset(&xh, 0, sizeof(xh));
 	if (rootdir)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
-	if (conffile)
-		strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+	if (confdir)
+		xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 	xh.flags = flags;
 
 	if ((rv = xbps_init(&xh)) != 0) {
diff --git a/bin/xbps-pkgdb/xbps-pkgdb.8 b/bin/xbps-pkgdb/xbps-pkgdb.8
index 8ae96498..dbaf5ecc 100644
--- a/bin/xbps-pkgdb/xbps-pkgdb.8
+++ b/bin/xbps-pkgdb/xbps-pkgdb.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-PKGDB 8
 .Sh NAME
 .Nm xbps-pkgdb
@@ -36,8 +36,10 @@ Updates the pkgdb format to the latest version.
 .Bl -tag -width -x
 .It Fl a, Fl -all
 Process all registered packages, regardless of its state.
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl d, Fl -debug
 Enables extra debugging shown to stderr.
 .It Fl h, Fl -help
@@ -67,8 +69,8 @@ Shows the XBPS version.
 .El
 .Sh FILES
 .Bl -tag -width /var/db/xbps/.<pkgname>-files.plist
-.It Ar /etc/xbps/xbps.conf
-Default configuration file.
+.It Ar /etc/xbps.d
+Default configuration directory.
 .It Ar /var/db/xbps/.<pkgname>-files.plist
 Package files metadata.
 .It Ar /var/db/xbps/pkgdb-0.38.plist
diff --git a/bin/xbps-query/list.c b/bin/xbps-query/list.c
index 8532dc93..f9847949 100644
--- a/bin/xbps-query/list.c
+++ b/bin/xbps-query/list.c
@@ -77,7 +77,7 @@ list_pkgs_in_dict(struct xbps_handle *xhp _unused,
 		assert(out);
 		snprintf(out, lpc->maxcols - 3,
 		    "%s %s", tmp, short_desc);
-		strncat(out, "...\n", lpc->maxcols);
+		xbps_strlcat(out, "...\n", sizeof(*out));
 		printf("%s", out);
 		free(out);
 	} else {
diff --git a/bin/xbps-query/main.c b/bin/xbps-query/main.c
index 897534dc..199b5e50 100644
--- a/bin/xbps-query/main.c
+++ b/bin/xbps-query/main.c
@@ -38,8 +38,8 @@ usage(bool fail)
 	fprintf(stdout,
 	    "Usage: xbps-query [OPTIONS] MODE [ARGUMENTS]\n"
 	    "\nOPTIONS\n"
-	    " -C --config <file>       Full path to configuration file\n"
-	    " -c --cachedir <dir>      Full path to cachedir\n"
+	    " -C --config <dir>        Path to confdir (xbps.d)\n"
+	    " -c --cachedir <dir>      Path to cachedir\n"
 	    " -d --debug               Debug mode shown to stderr\n"
 	    " -h --help                Print help usage\n"
 	    " -p --property PROP[,...] Show properties for PKGNAME\n"
@@ -99,13 +99,13 @@ main(int argc, char **argv)
 		{ NULL, 0, NULL, 0 },
 	};
 	struct xbps_handle xh;
-	const char *pkg, *rootdir, *cachedir, *conffile, *props;
+	const char *pkg, *rootdir, *cachedir, *confdir, *props;
 	int c, flags, rv;
 	bool list_pkgs, list_repos, orphans, own;
 	bool list_manual, list_hold, show_prop, show_files, show_deps, show_rdeps;
 	bool show, pkg_search, regex, repo_mode, opmode, fulldeptree;
 
-	rootdir = cachedir = conffile = props = pkg = NULL;
+	rootdir = cachedir = confdir = props = pkg = NULL;
 	flags = rv = c = 0;
 	list_pkgs = list_repos = list_hold = orphans = pkg_search = own = false;
 	list_manual = show_prop = show_files = false;
@@ -117,7 +117,7 @@ main(int argc, char **argv)
 	while ((c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1) {
 		switch (c) {
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'c':
 			cachedir = optarg;
@@ -214,11 +214,11 @@ main(int argc, char **argv)
 	 * Initialize libxbps.
 	 */
 	if (rootdir)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
 	if (cachedir)
-		strncpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
-	if (conffile)
-		strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+		xbps_strlcpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
+	if (confdir)
+		xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 
 	xh.flags = flags;
 
diff --git a/bin/xbps-query/search.c b/bin/xbps-query/search.c
index 22c2f9cb..fc4091f4 100644
--- a/bin/xbps-query/search.c
+++ b/bin/xbps-query/search.c
@@ -68,7 +68,7 @@ print_results(struct xbps_handle *xhp, struct search_data *sd)
 	for (unsigned int i = 0; i < xbps_array_count(sd->results); i++) {
 		xbps_array_get_cstring_nocopy(sd->results, i, &pkgver);
 		xbps_array_get_cstring_nocopy(sd->results, i+1, &desc);
-		strncpy(tmp, pkgver, sizeof(tmp));
+		xbps_strlcpy(tmp, pkgver, sizeof(tmp));
 		for (j = strlen(tmp); j < tlen; j++)
 			tmp[j] = ' ';
 
@@ -84,7 +84,7 @@ print_results(struct xbps_handle *xhp, struct search_data *sd)
 			assert(out);
 			snprintf(out, sd->maxcols-3, "%s %s %s",
 			    inststr, tmp, desc);
-			strncat(out, "...\n", sd->maxcols);
+			xbps_strlcat(out, "...\n", sizeof(*out));
 			printf("%s", out);
 			free(out);
 		} else {
diff --git a/bin/xbps-query/xbps-query.8 b/bin/xbps-query/xbps-query.8
index 806dcbd4..d2e35c1a 100644
--- a/bin/xbps-query/xbps-query.8
+++ b/bin/xbps-query/xbps-query.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-QUERY 8
 .Sh NAME
 .Nm xbps-query
@@ -53,10 +53,14 @@ Example:
 The first repository matching the package expression wins.
 .Sh OPTIONS
 .Bl -tag -width -x
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl c, Fl -cachedir Ar dir
-Specifies a full path to the cache directory, where binary packages are stored.
+Specifies a path to the cache directory, where binary packages are stored.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl d, Fl -debug
 Enables extra debugging shown to stderr.
 .It Fl h, Fl -help
@@ -224,8 +228,8 @@ the native architecture).
 .El
 .Sh FILES
 .Bl -tag -width /var/db/xbps/.<pkgname>-files.plist
-.It Ar /etc/xbps/xbps.conf
-Default configuration file.
+.It Ar /etc/xbps.d
+Default configuration directory.
 .It Ar /var/db/xbps/.<pkgname>-files.plist
 Package files metadata.
 .It Ar /var/db/xbps/pkgdb-0.38.plist
diff --git a/bin/xbps-reconfigure/main.c b/bin/xbps-reconfigure/main.c
index cbb37ed0..e7bee42a 100644
--- a/bin/xbps-reconfigure/main.c
+++ b/bin/xbps-reconfigure/main.c
@@ -40,7 +40,7 @@ usage(bool fail)
 	    "Usage: xbps-reconfigure [OPTIONS] [PKGNAME...]\n\n"
 	    "OPTIONS\n"
 	    " -a --all            Process all packages\n"
-	    " -C --config <file>  Full path to configuration file\n"
+	    " -C --config <dir>   Path to confdir (xbps.d)\n"
 	    " -d --debug          Debug mode shown to stderr\n"
 	    " -f --force          Force reconfiguration\n"
 	    " -h --help           Print usage help\n"
@@ -104,7 +104,7 @@ main(int argc, char **argv)
 		{ NULL, 0, NULL, 0 }
 	};
 	struct xbps_handle xh;
-	const char *conffile = NULL, *rootdir = NULL;
+	const char *confdir = NULL, *rootdir = NULL;
 	int c, i, rv, flags = 0;
 	bool all = false;
 
@@ -114,7 +114,7 @@ main(int argc, char **argv)
 			all = true;
 			break;
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'd':
 			flags |= XBPS_FLAG_DEBUG;
@@ -146,9 +146,9 @@ main(int argc, char **argv)
 	memset(&xh, 0, sizeof(xh));
 	xh.state_cb = state_cb;
 	if (rootdir)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
-	if (conffile)
-		strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+	if (confdir)
+		xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 
 	xh.flags = flags;
 
diff --git a/bin/xbps-reconfigure/xbps-reconfigure.8 b/bin/xbps-reconfigure/xbps-reconfigure.8
index 3ba8440f..711bda75 100644
--- a/bin/xbps-reconfigure/xbps-reconfigure.8
+++ b/bin/xbps-reconfigure/xbps-reconfigure.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-RECONFIGURE 8
 .Sh NAME
 .Nm xbps-reconfigure
@@ -35,8 +35,10 @@ option is specified.
 .Bl -tag -width -x
 .It Fl a, Fl -all
 Configures all packages.
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl d, Fl -debug
 Enables extra debugging shown to stderr.
 .It Fl f, Fl -force
@@ -44,7 +46,7 @@ Forcefully reconfigure package even if it was configured previously.
 .It Fl h, Fl -help
 Show the help usage.
 .It Fl r, Fl -rootdir Ar dir
-Specifies a full path for the target root directory.
+Specifies a path for the target root directory.
 .It Fl v, Fl -verbose
 Enables verbose messages.
 .It Fl V, Fl -version
@@ -52,8 +54,8 @@ Shows the XBPS version.
 .El
 .Sh FILES
 .Bl -tag -width /var/db/xbps/.<pkgname>-files.plist
-.It Ar /etc/xbps/xbps.conf
-Default configuration file.
+.It Ar /etc/xbps.d
+Default configuration directory.
 .It Ar /var/db/xbps/.<pkgname>.plist
 Package files metadata.
 .It Ar /var/db/xbps/pkgdb-0.38.plist
diff --git a/bin/xbps-remove/main.c b/bin/xbps-remove/main.c
index 7b563282..831b02aa 100644
--- a/bin/xbps-remove/main.c
+++ b/bin/xbps-remove/main.c
@@ -45,8 +45,8 @@ usage(bool fail)
 	fprintf(stdout,
 	    "Usage: xbps-remove [OPTIONS] [PKGNAME...]\n\n"
 	    "OPTIONS\n"
-	    " -C --config <file>       Full path to configuration file\n"
-	    " -c --cachedir <dir>      Full path to cachedir\n"
+	    " -C --config <dir>        Path to confdir (xbps.d)\n"
+	    " -c --cachedir <dir>      Path to cachedir\n"
 	    " -d --debug               Debug mode shown to stderr\n"
 	    " -F --force-revdeps       Force package removal even with revdeps\n"
 	    " -f --force               Force package files removal\n"
@@ -181,13 +181,13 @@ main(int argc, char **argv)
 		{ NULL, 0, NULL, 0 }
 	};
 	struct xbps_handle xh;
-	const char *rootdir, *cachedir, *conffile;
+	const char *rootdir, *cachedir, *confdir;
 	int c, flags, rv;
 	bool yes, drun, recursive, ignore_revdeps, clean_cache;
 	bool orphans, reqby_force;
 	int maxcols;
 
-	rootdir = cachedir = conffile = NULL;
+	rootdir = cachedir = confdir = NULL;
 	flags = rv = 0;
 	drun = recursive = ignore_revdeps = clean_cache = false;
 	reqby_force = yes = orphans = false;
@@ -195,7 +195,7 @@ main(int argc, char **argv)
 	while ((c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1) {
 		switch (c) {
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'c':
 			cachedir = optarg;
@@ -251,11 +251,11 @@ main(int argc, char **argv)
 	memset(&xh, 0, sizeof(xh));
 	xh.state_cb = state_cb_rm;
 	if (rootdir)
-		strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+		xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
 	if (cachedir)
-		strncpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
-	if (conffile)
-		strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+		xbps_strlcpy(xh.cachedir, cachedir, sizeof(xh.cachedir));
+	if (confdir)
+		xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 
 	xh.flags = flags;
 
diff --git a/bin/xbps-remove/xbps-remove.8 b/bin/xbps-remove/xbps-remove.8
index fbff74a2..c75c9382 100644
--- a/bin/xbps-remove/xbps-remove.8
+++ b/bin/xbps-remove/xbps-remove.8
@@ -1,4 +1,4 @@
-.Dd September 30, 2014
+.Dd November 5, 2014
 .Dt XBPS-REMOVE 8
 .Sh NAME
 .Nm xbps-remove
@@ -58,10 +58,14 @@ Package metadata file is removed.
 Package is unregistered from package database.
 .Sh OPTIONS
 .Bl -tag -width -x
-.It Fl C, Fl -config Ar file
-Specifies a full path to the XBPS configuration file.
+.It Fl C, Fl -config Ar dir
+Specifies a path to the XBPS configuration directory.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl c, Fl -cachedir Ar dir
-Specifies a full path to the cache directory, where binary packages are stored.
+Specifies a path to the cache directory, where binary packages are stored.
+If the first character is not '\/' then it's a relative path of
+.Ar rootdir .
 .It Fl d, Fl -debug
 Enables extra debugging shown to stderr.
 .It Fl F, Fl -force-revdeps
@@ -92,8 +96,8 @@ Shows the XBPS version.
 .El
 .Sh FILES
 .Bl -tag -width /var/db/xbps/.<pkgname>-files.plist
-.It Ar /etc/xbps/xbps.conf
-Default configuration file.
+.It Ar /etc/xbps.d
+Default configuration directory.
 .It Ar /var/db/xbps/.<pkgname>-files.plist
 Package files metadata.
 .It Ar /var/db/xbps/pkgdb-0.38.plist
diff --git a/bin/xbps-uhelper/main.c b/bin/xbps-uhelper/main.c
index d7b6681e..01b86a36 100644
--- a/bin/xbps-uhelper/main.c
+++ b/bin/xbps-uhelper/main.c
@@ -103,14 +103,14 @@ main(int argc, char **argv)
 	xbps_dictionary_t dict;
 	struct xbps_handle xh;
 	struct xferstat xfer;
-	const char *version, *rootdir = NULL, *conffile = NULL;
+	const char *version, *rootdir = NULL, *confdir = NULL;
 	char *pkgname, *hash, *filename;
 	int flags = 0, c, rv = 0;
 
 	while ((c = getopt(argc, argv, "C:dr:V")) != -1) {
 		switch (c) {
 		case 'C':
-			conffile = optarg;
+			confdir = optarg;
 			break;
 		case 'r':
 			/* To specify the root directory */
@@ -146,9 +146,9 @@ main(int argc, char **argv)
 		xh.fetch_cb = fetch_file_progress_cb;
 		xh.fetch_cb_data = &xfer;
 		if (rootdir)
-			strncpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
-		if (conffile)
-			strncpy(xh.conffile, conffile, sizeof(xh.conffile));
+			xbps_strlcpy(xh.rootdir, rootdir, sizeof(xh.rootdir));
+		if (confdir)
+			xbps_strlcpy(xh.confdir, confdir, sizeof(xh.confdir));
 		if ((rv = xbps_init(&xh)) != 0) {
 			xbps_error_printf("xbps-uhelper: failed to "
 			    "initialize libxbps: %s.\n", strerror(rv));
diff --git a/configure b/configure
index d1eb9b0c..33f423b9 100755
--- a/configure
+++ b/configure
@@ -61,7 +61,7 @@ for x; do
 	--host) HOST=$var;;
 	--target) TARGET=$var;;
 	--includedir) INCLUDEDIR=$var;;
-	--sysconfdir) ETCDIR=$var;;
+	--sysconfdir) SYSCONFDIR=$var;;
 	--localstatedir) LOCALSTATEDIR=$var;;
 	--libdir) LIBDIR=$var;;
 	--datadir|--infodir) ;; # ignore autotools
@@ -86,7 +86,6 @@ done
 : ${SHAREDIR:=${EPREFIX}/share}
 : ${MANDIR:=${EPREFIX}/share/man}
 : ${INCLUDEDIR:=${EPREFIX}/include}
-: ${ETCDIR:=${PREFIX}/etc}
 : ${PKGCONFIGDIR:=${LIBDIR}/pkgconfig}
 : ${TESTSDIR:=${EPREFIX}/tests}
 : ${LOCALSTATEDIR:=/var}
@@ -154,7 +153,7 @@ echo "PKGCONFIGDIR ?= $PKGCONFIGDIR" >>$CONFIG_MK
 echo "TESTSDIR ?= $TESTSDIR" >>$CONFIG_MK
 echo "DBDIR ?= $DBDIR" >>$CONFIG_MK
 
-ETCDIR="${ETCDIR}/xbps"
+ETCDIR="${SYSCONFDIR}/xbps.d"
 echo "ETCDIR ?= $ETCDIR" >>$CONFIG_MK
 
 [ -z "$DEBUG" ] && DEBUG=no
@@ -186,6 +185,7 @@ echo "CFLAGS = -O2 -pthread" >>$CONFIG_MK
 echo "LDFLAGS =  	-L\$(TOPDIR)/lib" >>$CONFIG_MK
 echo "CPPFLAGS = 	-I. -I\$(TOPDIR) -I\$(TOPDIR)/include" >>$CONFIG_MK
 echo "CPPFLAGS +=	-DXBPS_SYSCONF_PATH=\\\"${ETCDIR}\\\"" >>$CONFIG_MK
+echo "CPPFLAGS +=	-DXBPS_SYSDEFCONF_PATH=\\\"${SHAREDIR}/xbps.d\\\"" >>$CONFIG_MK
 echo "CPPFLAGS +=	-DXBPS_VERSION=\\\"${VERSION}\\\"" >>$CONFIG_MK
 echo "CPPFLAGS +=	-D_unused=\"__attribute__((__unused__))\"" >>$CONFIG_MK
 
diff --git a/data/Makefile b/data/Makefile
index 413385b8..064316e6 100644
--- a/data/Makefile
+++ b/data/Makefile
@@ -15,21 +15,23 @@ install:
 	install -m644 $(PCFILE) $(DESTDIR)$(PKGCONFIGDIR)
 	install -d $(DESTDIR)/$(DBDIR)/keys
 	install -m644 *.plist $(DESTDIR)/$(DBDIR)/keys
-	install -d $(DESTDIR)/$(PREFIX)/share/xbps/repo.d
-	install -m644 repod-main.conf $(DESTDIR)/$(PREFIX)/share/xbps/repo.d/00-main.conf
-	install -d $(DESTDIR)/$(PREFIX)/share/zsh/site-functions
-	install -m644 _xbps* $(DESTDIR)/$(PREFIX)/share/zsh/site-functions
-	install -d $(DESTDIR)/$(PREFIX)/share/bash-completion/completions
-	install -m644 xbps.bash $(DESTDIR)/$(PREFIX)/share/bash-completion/completions/xbps
+	install -d $(DESTDIR)/$(SHAREDIR)/xbps.d
+	install -m644 repod-main.conf $(DESTDIR)/$(SHAREDIR)/xbps.d/00-repository-main.conf
+	install -m644 xbps.conf $(DESTDIR)/$(SHAREDIR)/xbps.d/xbps.conf
+	install -d $(DESTDIR)/$(SHAREDIR)/zsh/site-functions
+	install -m644 _xbps* $(DESTDIR)/$(SHAREDIR)/zsh/site-functions
+	install -d $(DESTDIR)/$(SHAREDIR)/bash-completion/completions
+	install -m644 xbps.bash $(DESTDIR)/$(SHAREDIR)/bash-completion/completions/xbps
 	for file in xbps-checkvers xbps-create xbps-dgraph xbps-install \
 		xbps-pkgdb xbps-query xbps-reconfigure xbps-remove xbps-rindex; do \
-		ln -sf xbps $(DESTDIR)/$(PREFIX)/share/bash-completion/completions/$$file; \
+		ln -sf xbps $(DESTDIR)/$(SHAREDIR)/bash-completion/completions/$$file; \
 	done
 
 .PHONY: uninstall
 uninstall:
 	-rm -f $(DESTDIR)$(PKGCONFIGDIR)/$(PCFILE)
-	-rm -f $(DESTDIR)$(PREFIX)/share/xbps/repo.d/main.conf
+	-rm -f $(DESTDIR)$(SHAREDIR)/xbps.d/00-repository-main.conf
+	-rm -f $(DESTDIR)$(SHAREDIR)/xbps.d/xbps.conf
 
 
 .PHONY: clean
diff --git a/etc/xbps.conf b/data/xbps.conf
similarity index 78%
rename from etc/xbps.conf
rename to data/xbps.conf
index cfe90b6a..eaf9b267 100644
--- a/etc/xbps.conf
+++ b/data/xbps.conf
@@ -18,14 +18,6 @@
 # The `repository' keyword defines a repository. A complete URL or absolute
 # path to a local directory can be used.
 #
-# The default system repository directory "<rootdir>/usr/share/xbps/repo.d"
-# contains the system repository configuration files.
-#
-# Files on that system directory can be overrided in "<rootdir>/etc/xbps/repo.d"
-# bearing the same file name, i.e:
-#
-#  - /etc/xbps/repo.d/main.conf overrides /usr/share/xbps/repo.d/main.conf
-#
 # Local or remote repositories are accepted.
 #
 #  - Local repositories expect an absolute path to the directory that stores
@@ -37,8 +29,11 @@
 #    to the tail of the list.
 #
 # The "repository" keyword can be used to include additional repositories in
-# addition to the files available in /etc/xbps/repo.d/*.conf and
-# /usr/share/xbps/repo.d/*.conf.
+# addition to the files available in /etc/xbps.d/*.conf and
+# /usr/share/xbps.d/*.conf.
+#
+# syntax: <protocol>://<url>[:<port>]/<doc> [remote]
+# syntax: <abspath> [local]
 #
 # Example:
 #	repository=http://foo.example.org/dir
@@ -65,9 +60,6 @@
 # specified files. Files must be specified with absolute pathnames or via
 # file globbing.
 #
-# The system preserve directory is set to <rootdir>/usr/share/xbps/preserve.d.
-# The configuration preserve directory is set to <rootdir>/etc/xbps/virtualpkg.d.
-#
 # Files bearing the same name in the configuration directory override the
 # ones from the system directory.
 #
@@ -85,9 +77,6 @@
 #   separated by a dash, i.e 'foo-1.0_1".
 # - <realpkgname> means a real package name (without any version).
 #
-# The system virtualpkg directory is set to <rootdir>/usr/share/xbps/virtualpkg.d.
-# The configuration virtualpkg directory is set to <rootdir>/etc/xbps/virtualpkg.d.
-#
 # Files bearing the same name in the configuration directory override the
 # ones from the system directory.
 #
diff --git a/etc/Makefile b/etc/Makefile
deleted file mode 100644
index e5d3bd25..00000000
--- a/etc/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
--include ../config.mk
-
-CONF_FILES =	xbps.conf
-
-.PHONY: all
-all:
-
-.PHONY: install
-install:
-	install -d $(DESTDIR)$(ETCDIR)
-	for f in $(CONF_FILES); do				\
-		if [ ! -f $(DESTDIR)$(ETCDIR)/$$f ]; then	\
-			install -m644 $$f $(DESTDIR)$(ETCDIR);	\
-		fi;						\
-	done
-
-.PHONY: uninstall
-uninstall:
-
-.PHONY: clean
-clean:
diff --git a/include/xbps.h.in b/include/xbps.h.in
index 0708f5c0..614e94e8 100644
--- a/include/xbps.h.in
+++ b/include/xbps.h.in
@@ -48,7 +48,7 @@
  *
  * This header documents the full API for the XBPS Library.
  */
-#define XBPS_API_VERSION	"20141104"
+#define XBPS_API_VERSION	"20141105"
 
 #ifndef XBPS_VERSION
  #define XBPS_VERSION		"UNSET"
@@ -68,12 +68,12 @@
  * @def XBPS_SYSCONF_PATH
  * Default configuration PATH to find XBPS_CONF_PLIST.
  */
-#define XBPS_SYSDIR            "/xbps"
+#define XBPS_SYSDIR            "/xbps.d"
 #ifndef XBPS_SYSCONF_PATH
 # define XBPS_SYSCONF_PATH      "/etc" XBPS_SYSDIR
 #endif
 #ifndef XBPS_SYSDEFCONF_PATH
-# define XBPS_SYSDEFCONF_PATH	"usr/share" XBPS_SYSDIR
+# define XBPS_SYSDEFCONF_PATH	"/usr/share" XBPS_SYSDIR
 #endif
 
 /** 
@@ -88,42 +88,6 @@
  */
 #define XBPS_CACHE_PATH		"var/cache/xbps"
 
-/**
- * @def XBPS_VPKG_PATH
- * Configuration virtualpkg directory to store virtualpkg configuration files.
- */
-#define XBPS_VPKG_PATH		XBPS_SYSCONF_PATH "/virtualpkg.d"
-
-/**
- * @def XBPS_SYS_VPKG_PATH
- * System virtualpkg PATH to store virtualpkg configuration files.
- */
-#define XBPS_SYS_VPKG_PATH	XBPS_SYSDEFCONF_PATH "/virtualpkg.d"
-
-/**
- * @def XBPS_REPOD_PATH
- * Configuration directory to store repository configuration files.
- */
-#define XBPS_REPOD_PATH 	XBPS_SYSCONF_PATH "/repo.d"
-
-/**
- * @def XBPS_SYS_REPOD_PATH
- * System directory to store repository configuration files.
- */
-#define XBPS_SYS_REPOD_PATH 	XBPS_SYSDEFCONF_PATH "/repo.d"
-
-/**
- * @def XBPS_PRESERVED_PATH
- * Configuration directory to store preserve configuration files.
- */
-#define XBPS_PRESERVED_PATH 	XBPS_SYSCONF_PATH "/preserve.d"
-
-/**
- * @def XBPS_SYS_PRESERVED_PATH
- * System directory to store preserve configuration files.
- */
-#define XBPS_SYS_PRESERVED_PATH XBPS_SYSDEFCONF_PATH "/preserve.d"
-
 /**
  * @def XBPS_PKGDB
  * Filename for the package database.
@@ -160,12 +124,6 @@
  */
 #define XBPS_REPOIDX_META 	"index-meta.plist"
 
-/**
- * @def XBPS_CONF_DEF
- * Filename for the XBPS plist configuration file.
- */
-#define XBPS_CONF_DEF		XBPS_SYSCONF_PATH "/xbps.conf"
-
 /**
  * @def XBPS_FLAG_VERBOSE
  * Verbose flag that can be used in the function callbacks to alter
@@ -586,11 +544,11 @@ struct xbps_handle {
 	 */
 	const char *target_arch;
 	/**
-	 * @var conffile
+	 * @var confdir
 	 *
-	 * Full path to the xbps configuration file.
+	 * Full path to the xbps configuration directory.
 	 */
-	char conffile[XBPS_MAXPATH];
+	char confdir[XBPS_MAXPATH];
 	/**
 	 * @var rootdir
 	 *
@@ -1834,7 +1792,8 @@ bool xbps_pkg_arch_match(struct xbps_handle *xhp,
  * @return A negative number is returned on error, 0 otherwise.
  */
 int xbps_humanize_number(char *buf, int64_t bytes);
-
+size_t xbps_strlcat(char *dest, const char *src, size_t siz);
+size_t xbps_strlcpy(char *dest, const char *src, size_t siz);
 /**
  * Tests if pkgver is reverted by pkg
  *
diff --git a/lib/initend.c b/lib/initend.c
index f9b9bbc5..697c64d5 100644
--- a/lib/initend.c
+++ b/lib/initend.c
@@ -45,7 +45,7 @@
 #pragma clang diagnostic ignored "-Wformat-nonliteral"
 #endif
 
-static int parse_file(struct xbps_handle *, const char *, const char *, bool, bool);
+static int parse_file(struct xbps_handle *, const char *, const char *, bool);
 
 /**
  * @file lib/initend.c
@@ -191,14 +191,14 @@ parse_option(char *buf, char **k, char **v)
 }
 
 static int
-parse_files_glob(struct xbps_handle *xhp, const char *cwd, const char *path, bool nested, bool vpkgconf)
+parse_files_glob(struct xbps_handle *xhp, const char *cwd, const char *path, bool nested)
 {
 	glob_t globbuf;
 	int rv = 0;
 
 	glob(path, 0, NULL, &globbuf);
 	for (size_t i = 0; i < globbuf.gl_pathc; i++) {
-		if ((rv = parse_file(xhp, cwd, globbuf.gl_pathv[i], nested, vpkgconf)) != 0)
+		if ((rv = parse_file(xhp, cwd, globbuf.gl_pathv[i], nested)) != 0)
 			break;
 	}
 	globfree(&globbuf);
@@ -207,7 +207,7 @@ parse_files_glob(struct xbps_handle *xhp, const char *cwd, const char *path, boo
 }
 
 static int
-parse_file(struct xbps_handle *xhp, const char *cwd, const char *path, bool nested, bool vpkgconf)
+parse_file(struct xbps_handle *xhp, const char *cwd, const char *path, bool nested)
 {
 	FILE *fp;
 	char tmppath[XBPS_MAXPATH] = {0};
@@ -222,9 +222,7 @@ parse_file(struct xbps_handle *xhp, const char *cwd, const char *path, bool nest
 		return rv;
 	}
 
-	if (!vpkgconf) {
-		xbps_dbg_printf(xhp, "Parsing configuration file: %s\n", path);
-	}
+	xbps_dbg_printf(xhp, "Parsing configuration file: %s\n", path);
 
 	while ((nread = getline(&line, &len, fp)) != -1) {
 		char *p, *k, *v;
@@ -281,7 +279,7 @@ parse_file(struct xbps_handle *xhp, const char *cwd, const char *path, bool nest
 			xbps_dbg_printf(xhp, "cannot chdir to %s: %s\n", cfcwd, strerror(rv));
 			return rv;
 		}
-		if ((rv = parse_files_glob(xhp, cwd, v, true, false)) != 0)
+		if ((rv = parse_files_glob(xhp, cwd, v, true)) != 0)
 			break;
 
 	}
@@ -292,10 +290,10 @@ parse_file(struct xbps_handle *xhp, const char *cwd, const char *path, bool nest
 }
 
 static int
-parse_dir(struct xbps_handle *xhp, const char *cwd, const char *dir, const char *confdir, bool vpkg)
+parse_dir(struct xbps_handle *xhp, const char *cwd, const char *dir, const char *confdir)
 {
 	struct dirent **namelist;
-	char *ext, ldir[PATH_MAX], conf[PATH_MAX];
+	char *ext, conf[PATH_MAX];
 	int i, n, rv = 0;
 
 	if (dir == NULL)
@@ -304,11 +302,9 @@ parse_dir(struct xbps_handle *xhp, const char *cwd, const char *dir, const char
 	 * Read all configuration files stored in the system
 	 * foo.d directory.
 	 */
-	snprintf(ldir, sizeof(ldir), "%s/%s",
-		strcmp(xhp->rootdir, "/") ? xhp->rootdir : "", dir);
-	xbps_dbg_printf(xhp, "Processing system directory: %s\n", ldir);
+	xbps_dbg_printf(xhp, "Processing system directory: %s\n", dir);
 
-	if ((n = scandir(ldir, &namelist, 0, alphasort)) < 0)
+	if ((n = scandir(dir, &namelist, 0, alphasort)) < 0)
 		goto stage2;
 
 	for (i = 0; i < n; i++) {
@@ -323,20 +319,20 @@ parse_dir(struct xbps_handle *xhp, const char *cwd, const char *dir, const char
 			continue;
 		}
 		if (strcmp(ext, ".conf") && strcmp(ext, ".vpkg")) {
-			xbps_dbg_printf(xhp, "%s: ignoring %s\n", ldir, namelist[i]->d_name);
+			xbps_dbg_printf(xhp, "%s: ignoring %s\n", dir, namelist[i]->d_name);
 			free(namelist[i]);
 			continue;
 		}
 		/* if the same file exists in configuration directory, ignore it */
-		snprintf(conf, sizeof(conf), "%s/%s/%s", xhp->rootdir, confdir, namelist[i]->d_name);
+		snprintf(conf, sizeof(conf), "%s/%s", confdir, namelist[i]->d_name);
 		if (access(conf, R_OK) == 0) {
-			xbps_dbg_printf(xhp, "%s: ignoring %s (exists in confdir)\n", ldir, namelist[i]->d_name);
+			xbps_dbg_printf(xhp, "%s: ignoring %s (exists in confdir)\n", dir, namelist[i]->d_name);
 			free(namelist[i]);
 			continue;
 		}
 		/* parse conf file */
-		snprintf(conf, sizeof(conf), "%s/%s", ldir, namelist[i]->d_name);
-		if ((rv = parse_file(xhp, cwd, conf, false, vpkg)) != 0) {
+		snprintf(conf, sizeof(conf), "%s/%s", dir, namelist[i]->d_name);
+		if ((rv = parse_file(xhp, cwd, conf, false)) != 0) {
 			free(namelist[i]);
 			break;
 		}
@@ -352,11 +348,9 @@ stage2:
 	/*
 	 * Read all configuration files stored in the configuration foo.d directory.
 	 */
-	snprintf(ldir, sizeof(ldir), "%s%s",
-		strcmp(xhp->rootdir, "/") ? xhp->rootdir : "", confdir);
-	xbps_dbg_printf(xhp, "Processing configuration directory: %s\n", ldir);
+	xbps_dbg_printf(xhp, "Processing configuration directory: %s\n", confdir);
 
-	if ((n = scandir(ldir, &namelist, 0, alphasort)) < 0)
+	if ((n = scandir(confdir, &namelist, 0, alphasort)) < 0)
 		return 0;
 
 	for (i = 0; i < n; i++) {
@@ -371,13 +365,13 @@ stage2:
 			continue;
 		}
 		if (strcmp(ext, ".conf") && strcmp(ext, ".vpkg")) {
-			xbps_dbg_printf(xhp, "%s: ignoring %s\n", ldir, namelist[i]->d_name);
+			xbps_dbg_printf(xhp, "%s: ignoring %s\n", confdir, namelist[i]->d_name);
 			free(namelist[i]);
 			continue;
 		}
 		/* parse conf file */
-		snprintf(conf, sizeof(conf), "%s/%s", ldir, namelist[i]->d_name);
-		if ((rv = parse_file(xhp, cwd, conf, false, vpkg)) != 0) {
+		snprintf(conf, sizeof(conf), "%s/%s", confdir, namelist[i]->d_name);
+		if ((rv = parse_file(xhp, cwd, conf, false)) != 0) {
 			free(namelist[i]);
 			break;
 		}
@@ -391,7 +385,7 @@ int
 xbps_init(struct xbps_handle *xhp)
 {
 	struct utsname un;
-	char cwd[PATH_MAX-1], *buf;
+	char cwd[PATH_MAX-1], sysconfdir[XBPS_MAXPATH], *buf;
 	const char *repodir, *native_arch;
 	int rv;
 
@@ -401,14 +395,6 @@ xbps_init(struct xbps_handle *xhp)
 	if (getcwd(cwd, sizeof(cwd)) == NULL)
 		return ENOTSUP;
 
-	/* set conffile */
-	if (xhp->conffile[0] == '\0') {
-		snprintf(xhp->conffile, sizeof(xhp->conffile), XBPS_CONF_DEF);
-	} else {
-		buf = strdup(xhp->conffile);
-		snprintf(xhp->conffile, sizeof(xhp->conffile), "%s/%s", cwd, buf);
-		free(buf);
-	}
 	/* Set rootdir */
 	if (xhp->rootdir[0] == '\0') {
 		xhp->rootdir[0] = '/';
@@ -418,11 +404,7 @@ xbps_init(struct xbps_handle *xhp)
 		snprintf(xhp->rootdir, sizeof(xhp->rootdir), "%s/%s", cwd, buf);
 		free(buf);
 	}
-	/* parse configuration file */
 	xbps_dbg_printf(xhp, "%s\n", XBPS_RELVER);
-	if ((rv = parse_file(xhp, cwd, xhp->conffile, false, false)) != 0) {
-		xbps_dbg_printf(xhp, "Using built-in defaults\n");
-	}
 	/* Set cachedir */
 	if (xhp->cachedir[0] == '\0') {
 		snprintf(xhp->cachedir, sizeof(xhp->cachedir),
@@ -447,17 +429,22 @@ xbps_init(struct xbps_handle *xhp)
 		    "%s/%s", strcmp(xhp->rootdir, "/") ? xhp->rootdir : "", buf);
 		free(buf);
 	}
-	/* process virtualpkg.d dirs */
-	if ((rv = parse_dir(xhp, cwd, XBPS_SYS_VPKG_PATH, XBPS_VPKG_PATH, true)) != 0)
-		return rv;
-
-	/* process repo.d dirs */
-	if ((rv = parse_dir(xhp, cwd, XBPS_SYS_REPOD_PATH, XBPS_REPOD_PATH, false)) != 0)
-		return rv;
-
-	/* process preserve.d dirs */
-	if ((rv = parse_dir(xhp, cwd, XBPS_SYS_PRESERVED_PATH, XBPS_PRESERVED_PATH, false)) != 0)
-		return rv;
+	/* set confdir */
+	if (xhp->confdir[0] == '\0') {
+		snprintf(xhp->confdir, sizeof(xhp->confdir),
+		    "%s%s", strcmp(xhp->rootdir, "/") ? xhp->rootdir : "",
+		    XBPS_SYSCONF_PATH);
+	} else if (xhp->confdir[0] != '/') {
+		/* relative path */
+		buf = strdup(xhp->confdir);
+		snprintf(xhp->confdir, sizeof(xhp->confdir),
+		    "%s/%s", strcmp(xhp->rootdir, "/") ? xhp->rootdir : "", buf);
+		free(buf);
+	}
+	/* set sysconfdir */
+	snprintf(sysconfdir, sizeof(sysconfdir),
+	    "%s%s", strcmp(xhp->rootdir, "/") ? xhp->rootdir : "",
+	    XBPS_SYSDEFCONF_PATH);
 
 	xhp->target_arch = getenv("XBPS_TARGET_ARCH");
 	if ((native_arch = getenv("XBPS_ARCH")) != NULL) {
@@ -470,9 +457,15 @@ xbps_init(struct xbps_handle *xhp)
 
 	xbps_fetch_set_cache_connection(XBPS_FETCH_CACHECONN, XBPS_FETCH_CACHECONN_HOST);
 
+	/* process xbps.d */
+	if ((rv = parse_dir(xhp, cwd, sysconfdir, xhp->confdir)) != 0)
+		return rv;
+
 	xbps_dbg_printf(xhp, "rootdir=%s\n", xhp->rootdir);
 	xbps_dbg_printf(xhp, "metadir=%s\n", xhp->metadir);
 	xbps_dbg_printf(xhp, "cachedir=%s\n", xhp->cachedir);
+	xbps_dbg_printf(xhp, "confdir=%s\n", xhp->confdir);
+	xbps_dbg_printf(xhp, "sysconfdir=%s\n", sysconfdir);
 	xbps_dbg_printf(xhp, "syslog=%s\n", xhp->flags & XBPS_FLAG_DISABLE_SYSLOG ? "false" : "true");
 	xbps_dbg_printf(xhp, "Architecture: %s\n", xhp->native_arch);
 	xbps_dbg_printf(xhp, "Target Architecture: %s\n", xhp->target_arch);
diff --git a/lib/package_script.c b/lib/package_script.c
index 3a9b3168..de27459c 100644
--- a/lib/package_script.c
+++ b/lib/package_script.c
@@ -98,7 +98,7 @@ xbps_pkg_exec_buffer(struct xbps_handle *xhp,
 
 	rv = xbps_file_exec(xhp, fpath, action, pkgname, version,
 			    update ? "yes" : "no",
-			    xhp->conffile, xhp->native_arch, NULL);
+			    "no", xhp->native_arch, NULL);
 	free(pkgname);
 
 out:
diff --git a/lib/transaction_ops.c b/lib/transaction_ops.c
index b4a9c053..b1496041 100644
--- a/lib/transaction_ops.c
+++ b/lib/transaction_ops.c
@@ -273,7 +273,6 @@ xbps_transaction_remove_pkg(struct xbps_handle *xhp,
 	xbps_array_t pkgs, orphans, orphans_pkg, reqby;
 	xbps_object_t obj;
 	const char *pkgver;
-	unsigned int count;
 	int rv = 0;
 
 	assert(pkgname != NULL);
@@ -305,9 +304,8 @@ xbps_transaction_remove_pkg(struct xbps_handle *xhp,
 	if (xbps_object_type(orphans) != XBPS_TYPE_ARRAY)
 		return EINVAL;
 
-	count = xbps_array_count(orphans);
-	while (count--) {
-		obj = xbps_array_get(orphans, count);
+	for (unsigned int i = 0; i < xbps_array_count(orphans); i++) {
+		obj = xbps_array_get(orphans, i);
 		xbps_dictionary_get_cstring_nocopy(obj, "pkgver", &pkgver);
 		xbps_dictionary_set_cstring_nocopy(obj, "transaction", "remove");
 		if ((rv = xbps_transaction_store(xhp, pkgs, obj, false)) != 0)
@@ -353,11 +351,10 @@ xbps_transaction_autoremove_pkgs(struct xbps_handle *xhp)
 	xbps_array_t orphans, pkgs;
 	xbps_object_t obj;
 	const char *pkgver;
-	unsigned int count;
 	int rv = 0;
 
 	orphans = xbps_find_pkg_orphans(xhp, NULL);
-	if ((count = xbps_array_count(orphans)) == 0) {
+	if (xbps_array_count(orphans) == 0) {
 		/* no orphans? we are done */
 		rv = ENOENT;
 		goto out;
@@ -372,8 +369,8 @@ xbps_transaction_autoremove_pkgs(struct xbps_handle *xhp)
 	/*
 	 * Add pkg orphan dictionary into the transaction pkgs queue.
 	 */
-	while (count--) {
-		obj = xbps_array_get(orphans, count);
+	for (unsigned int i = 0; i < xbps_array_count(orphans); i++) {
+		obj = xbps_array_get(orphans, i);
 		xbps_dictionary_get_cstring_nocopy(obj, "pkgver", &pkgver);
 		xbps_dictionary_set_cstring_nocopy(obj,
 		    "transaction", "remove");
diff --git a/lib/util.c b/lib/util.c
index 2cb22918..9be13c87 100644
--- a/lib/util.c
+++ b/lib/util.c
@@ -423,6 +423,18 @@ xbps_humanize_number(char *buf, int64_t bytes)
 	    HN_AUTOSCALE, HN_DECIMAL|HN_NOSPACE);
 }
 
+size_t
+xbps_strlcat(char *dest, const char *src, size_t siz)
+{
+	return strlcat(dest, src, siz);
+}
+
+size_t
+xbps_strlcpy(char *dest, const char *src, size_t siz)
+{
+	return strlcpy(dest, src, siz);
+}
+
 /*
  * Check if pkg is explicitly marked to replace a specific installed version.
  */
diff --git a/tests/xbps/libxbps/config/1.include.conf b/tests/xbps/libxbps/config/1.include.cf
similarity index 100%
rename from tests/xbps/libxbps/config/1.include.conf
rename to tests/xbps/libxbps/config/1.include.cf
diff --git a/tests/xbps/libxbps/config/2.include.conf b/tests/xbps/libxbps/config/2.include.cf
similarity index 100%
rename from tests/xbps/libxbps/config/2.include.conf
rename to tests/xbps/libxbps/config/2.include.cf
diff --git a/tests/xbps/libxbps/config/Makefile b/tests/xbps/libxbps/config/Makefile
index 0535c274..65162999 100644
--- a/tests/xbps/libxbps/config/Makefile
+++ b/tests/xbps/libxbps/config/Makefile
@@ -3,6 +3,6 @@ TOPDIR = ../../../..
 
 TESTSSUBDIR = xbps/libxbps/config
 TEST = config_test
-EXTRA_FILES = Kyuafile xbps.conf xbps_nomatch.conf 1.include.conf 2.include.conf
+EXTRA_FILES = Kyuafile xbps.cf xbps_nomatch.cf 1.include.cf 2.include.cf
 
 include $(TOPDIR)/mk/test.mk
diff --git a/tests/xbps/libxbps/config/main.c b/tests/xbps/libxbps/config/main.c
index 5112ad7b..d371a32c 100644
--- a/tests/xbps/libxbps/config/main.c
+++ b/tests/xbps/libxbps/config/main.c
@@ -25,6 +25,8 @@
  */
 #include <atf-c.h>
 #include <xbps.h>
+#include <stdlib.h>
+#include <limits.h>
 
 ATF_TC(config_include_test);
 ATF_TC_HEAD(config_include_test, tc)
@@ -36,19 +38,40 @@ ATF_TC_BODY(config_include_test, tc)
 {
 	struct xbps_handle xh;
 	const char *tcsdir;
+	char *buf, *buf2, pwd[PATH_MAX];
 
 	/* get test source dir */
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
-	/* change dir to make sure relative paths won't match */
-	ATF_REQUIRE_EQ(chdir("/"), 0);
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
-	snprintf(xh.conffile, sizeof(xh.conffile), "%s/xbps.conf", tcsdir);
+	buf = getcwd(pwd, sizeof(pwd));
+
+	xbps_strlcpy(xh.rootdir, pwd, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, pwd, sizeof(xh.metadir));
+	snprintf(xh.confdir, sizeof(xh.confdir), "%s/xbps.d", pwd);
+
+	ATF_REQUIRE_EQ(xbps_mkpath(xh.confdir, 0755), 0);
+
+	buf = xbps_xasprintf("%s/xbps.cf", tcsdir);
+	buf2 = xbps_xasprintf("%s/xbps.d/xbps.conf", pwd);
+	ATF_REQUIRE_EQ(symlink(buf, buf2), 0);
+	free(buf);
+	free(buf2);
+
+	buf = xbps_xasprintf("%s/1.include.cf", tcsdir);
+	buf2 = xbps_xasprintf("%s/xbps.d/1.include.conf", pwd);
+	ATF_REQUIRE_EQ(symlink(buf, buf2), 0);
+	free(buf);
+	free(buf2);
+
+	buf = xbps_xasprintf("%s/2.include.cf", tcsdir);
+	buf2 = xbps_xasprintf("%s/xbps.d/2.include.conf", pwd);
+	ATF_REQUIRE_EQ(symlink(buf, buf2), 0);
+	free(buf);
+	free(buf2);
+
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
-
 	/* should contain both repositories defined in [12].include.conf */
 	ATF_REQUIRE_EQ(xbps_array_count(xh.repositories), 2);
 }
@@ -64,16 +87,26 @@ ATF_TC_BODY(config_include_nomatch_test, tc)
 {
 	struct xbps_handle xh;
 	const char *tcsdir;
+	char *buf, *buf2, pwd[PATH_MAX];
 
 	/* get test source dir */
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
-	/* change dir to make sure relative paths won't match */
-	ATF_REQUIRE_EQ(chdir("/"), 0);
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
-	strncpy(xh.conffile, "/xbps_nomatch.conf", sizeof(xh.conffile));
+	buf = getcwd(pwd, sizeof(pwd));
+
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	snprintf(xh.confdir, sizeof(xh.confdir), "%s/xbps.d", pwd);
+
+	ATF_REQUIRE_EQ(xbps_mkpath(xh.confdir, 0755), 0);
+
+	buf = xbps_xasprintf("%s/xbps_nomatch.cf", tcsdir);
+	buf2 = xbps_xasprintf("%s/xbps.d/nomatch.conf", pwd);
+	ATF_REQUIRE_EQ(symlink(buf, buf2), 0);
+	free(buf);
+	free(buf2);
+
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
diff --git a/tests/xbps/libxbps/config/xbps.conf b/tests/xbps/libxbps/config/xbps.cf
similarity index 100%
rename from tests/xbps/libxbps/config/xbps.conf
rename to tests/xbps/libxbps/config/xbps.cf
diff --git a/tests/xbps/libxbps/config/xbps_nomatch.conf b/tests/xbps/libxbps/config/xbps_nomatch.cf
similarity index 100%
rename from tests/xbps/libxbps/config/xbps_nomatch.conf
rename to tests/xbps/libxbps/config/xbps_nomatch.cf
diff --git a/tests/xbps/libxbps/find_pkg_obsoletes/main.c b/tests/xbps/libxbps/find_pkg_obsoletes/main.c
index be15dc23..922252f1 100644
--- a/tests/xbps/libxbps/find_pkg_obsoletes/main.c
+++ b/tests/xbps/libxbps/find_pkg_obsoletes/main.c
@@ -78,8 +78,7 @@ ATF_TC_BODY(find_pkg_obsoletes_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.conffile, "/tmp/unexistent.conf", sizeof(xh.conffile));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
         d1 = create_dict("files", "/etc/foo.conf");
diff --git a/tests/xbps/libxbps/find_pkg_orphans/main.c b/tests/xbps/libxbps/find_pkg_orphans/main.c
index 4c8011af..df8869fe 100644
--- a/tests/xbps/libxbps/find_pkg_orphans/main.c
+++ b/tests/xbps/libxbps/find_pkg_orphans/main.c
@@ -62,8 +62,8 @@ ATF_TC_BODY(find_pkg_orphans_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
 	a = xbps_array_create();
@@ -99,8 +99,8 @@ ATF_TC_BODY(find_all_orphans_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
 	pstr = xbps_string_create();
diff --git a/tests/xbps/libxbps/pkgdb/main.c b/tests/xbps/libxbps/pkgdb/main.c
index 3783b435..6e12dca9 100644
--- a/tests/xbps/libxbps/pkgdb/main.c
+++ b/tests/xbps/libxbps/pkgdb/main.c
@@ -42,8 +42,8 @@ ATF_TC_BODY(pkgdb_get_pkg_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
@@ -84,8 +84,8 @@ ATF_TC_BODY(pkgdb_get_virtualpkg_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
@@ -129,8 +129,8 @@ ATF_TC_BODY(pkgdb_get_pkg_revdeps_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
@@ -162,8 +162,8 @@ ATF_TC_BODY(pkgdb_pkg_reverts_test, tc)
 	tcsdir = atf_tc_get_config_var(tc, "srcdir");
 
 	memset(&xh, 0, sizeof(xh));
-	strncpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
-	strncpy(xh.metadir, tcsdir, sizeof(xh.metadir));
+	xbps_strlcpy(xh.rootdir, tcsdir, sizeof(xh.rootdir));
+	xbps_strlcpy(xh.metadir, tcsdir, sizeof(xh.metadir));
 	xh.flags = XBPS_FLAG_DEBUG;
 	ATF_REQUIRE_EQ(xbps_init(&xh), 0);
 
diff --git a/tests/xbps/libxbps/shell/preserve_files_test.sh b/tests/xbps/libxbps/shell/preserve_files_test.sh
index d2769258..3bb2402d 100644
--- a/tests/xbps/libxbps/shell/preserve_files_test.sh
+++ b/tests/xbps/libxbps/shell/preserve_files_test.sh
@@ -19,12 +19,13 @@ tc1_body() {
 	cd ..
 
 	mkdir -p root/usr/bin
+	mkdir -p root/xbps.d
 	echo "modified blahblah" > root/usr/bin/blah
 	echo "modified foofoo" > root/usr/bin/foo
 
-	echo "preserve=/usr/bin/*" > foo.conf
+	echo "preserve=/usr/bin/*" > root/xbps.d/foo.conf
 
-	xbps-install -C foo.conf -r root --repository=$PWD/some_repo -yd A
+	xbps-install -C xbps.d -r root --repository=$PWD/some_repo -yd A
 	atf_check_equal $? 0
 
 	rv=1
@@ -53,15 +54,16 @@ tc2_body() {
 	cd ..
 
 	mkdir -p root/usr/bin
+	mkdir -p root/xbps.d
 	echo "modified blahblah" > root/usr/bin/blah
 	echo "modified foofoo" > root/usr/bin/foo
 
-	printf "preserve=/usr/bin/blah\npreserve=/usr/bin/foo\n" > foo.conf
+	printf "preserve=/usr/bin/blah\npreserve=/usr/bin/foo\n" > root/xbps.d/foo.conf
 
 	echo "foo.conf" >&2
 	cat foo.conf >&2
 
-	xbps-install -C foo.conf -r root --repository=$PWD/some_repo -yd A
+	xbps-install -C xbps.d -r root --repository=$PWD/some_repo -yd A
 	atf_check_equal $? 0
 
 	rv=1
diff --git a/tests/xbps/libxbps/shell/scripts_test.sh b/tests/xbps/libxbps/shell/scripts_test.sh
index 41a86cdf..88c07299 100644
--- a/tests/xbps/libxbps/shell/scripts_test.sh
+++ b/tests/xbps/libxbps/shell/scripts_test.sh
@@ -41,7 +41,7 @@ script_nargs_body() {
 	rval=0
 	xbps-reconfigure -C empty.conf -r root -f A 2>out
 	out="$(cat out)"
-	expected="post A 1.0_1 no $(pwd)/empty.conf $(uname -m)"
+	expected="post A 1.0_1 no no $(uname -m)"
 	if [ "$out" != "$expected" ]; then
 		echo "out: '$out'"
 		echo "expected: '$expected'"
@@ -75,7 +75,7 @@ script_arch_body() {
 	rval=0
 	XBPS_ARCH=foo xbps-reconfigure -C empty.conf -r root -f A 2>out
 	out="$(cat out)"
-	expected="post A 1.0_1 no $(pwd)/empty.conf foo"
+	expected="post A 1.0_1 no no foo"
 	if [ "$out" != "$expected" ]; then
 		echo "out: '$out'"
 		echo "expected: '$expected'"