For those who have missed the initial email surrounding this topic, we are planning on packaging the base system with pkg(8) for 11.0-RELEASE. <SNIP>
I was successful in following your instructions and upgraded from 11-CURRENT r295677 to r296347 using pkg. Michael Jung
Index: ports-mgmt/pkg/files/patch-libpkg_pkg__config.c
===================================================================
--- ports-mgmt/pkg/files/patch-libpkg_pkg__config.c (nonexistent)
+++ ports-mgmt/pkg/files/patch-libpkg_pkg__config.c (working copy)
@@ -0,0 +1,15 @@
+--- libpkg/pkg_config.c.orig 2016-01-26 23:32:05 UTC
++++ libpkg/pkg_config.c
+@@ -390,6 +390,12 @@ static struct config_entry c[] = {
+ "VALID_URL_SCHEME",
+ "pkg+http,pkg+https,https,http,ftp,file,ssh",
+ },
++ {
++ PKG_BOOL,
++ "ALLOW_BASE_SHLIBS",
++ "NO",
++ "Enable base libraries analysis",
++ },
+ };
+
+ static bool parsed = false;
Index: ports-mgmt/pkg/files/patch-libpkg_pkg__elf.c
===================================================================
--- ports-mgmt/pkg/files/patch-libpkg_pkg__elf.c (nonexistent)
+++ ports-mgmt/pkg/files/patch-libpkg_pkg__elf.c (working copy)
@@ -0,0 +1,40 @@
+--- libpkg/pkg_elf.c.orig 2015-09-21 08:53:23 UTC
++++ libpkg/pkg_elf.c
+@@ -85,23 +85,28 @@ static int
+ filter_system_shlibs(const char *name, char *path, size_t pathlen)
+ {
+ const char *shlib_path;
++ bool packaging_base =
pkg_object_bool(pkg_config_get("ALLOW_BASE_SHLIBS"));
+
+- shlib_path = shlib_list_find_by_name(name);
+- if (shlib_path == NULL) {
+- /* dynamic linker could not resolve */
+- return (EPKG_FATAL);
++ if (!packaging_base) {
++ shlib_path = shlib_list_find_by_name(name);
++ if (shlib_path == NULL) {
++ /* dynamic linker could not resolve */
++ return (EPKG_FATAL);
++ }
+ }
+
+- /* match /lib, /lib32, /usr/lib and /usr/lib32 */
+- if (strncmp(shlib_path, "/lib", 4) == 0 ||
+- strncmp(shlib_path, "/usr/lib", 8) == 0)
+- return (EPKG_END); /* ignore libs from base */
++ if (!packaging_base) {
++ /* match /lib, /lib32, /usr/lib and /usr/lib32 */
++ if (strncmp(shlib_path, "/lib", 4) == 0 ||
++ strncmp(shlib_path, "/usr/lib", 8) == 0)
++ return (EPKG_END); /* ignore libs from base */
++ }
+
+ if (path != NULL)
+ strncpy(path, shlib_path, pathlen);
+
+ return (EPKG_OK);
+-}
++}
+
+ /* ARGSUSED */
+ static int
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