xbps-src: perform bootstrapping in two phases.

- binary-bootstrap unpacks all pkgs and configure base-files.
- after accessing the chroot for the first time all pkgs are configured.

This should fix the issue of ca-certificates not generating the certs.

xbps-src

@@ -284,7 +284,7 @@ install_bbootstrap() {
     mkdir -p $XBPS_MASTERDIR/var/db/xbps/keys
     cd $XBPS_MASTERDIR
     cp -f $XBPS_COMMONDIR/repo-keys/*.plist $XBPS_MASTERDIR/var/db/xbps/keys
-    ${_bootstrap_arch} $XBPS_INSTALL_CMD ${XBPS_INSTALL_ARGS:+-S $XBPS_INSTALL_ARGS} -y base-chroot${_subarch}
+    ${_bootstrap_arch} $XBPS_INSTALL_CMD ${XBPS_INSTALL_ARGS:+-S $XBPS_INSTALL_ARGS} -yU base-chroot${_subarch}
     if [ $? -ne 0 ]; then
         msg_error "Failed to install bootstrap packages!\n"
     fi
@@ -602,6 +602,10 @@ if [ -z "$IN_CHROOT" ]; then
     fi
 fi
 
+if [ -n "$IN_CHROOT" ]; then
+    xbps-reconfigure -a &>/dev/null
+fi
+
 #
 # Main switch.
 #