Index: git-r3.eclass
===================================================================
RCS file: /var/cvsroot/gentoo-x86/eclass/git-r3.eclass,v
retrieving revision 1.49
diff -u -B -r1.49 git-r3.eclass
--- git-r3.eclass	22 Jun 2015 08:39:36 -0000	1.49
+++ git-r3.eclass	26 Jun 2015 20:39:05 -0000
@@ -710,16 +710,23 @@
 			local subname=${submodules[0]}
 			local url=${submodules[1]}
 			local path=${submodules[2]}
-			local commit=$(git rev-parse "${local_ref}:${path}")
 
-			if [[ ! ${commit} ]]; then
-				die "Unable to get commit id for submodule ${subname}"
-			fi
+			# use only submodules for which path does exist
+			# (this is in par with 'git submodule'), bug #551100
+			# note: git cat-file does not work for submodules
+			if [[ $(git ls-tree -d "${local_ref}" "${path}") ]]
+			then
+				local commit=$(git rev-parse "${local_ref}:${path}" || die)
+
+				if [[ ! ${commit} ]]; then
+					die "Unable to get commit id for submodule ${subname}"
+				fi
 
-			local subrepos
-			_git-r3_set_subrepos "${url}" "${repos[@]}"
+				local subrepos
+				_git-r3_set_subrepos "${url}" "${repos[@]}"
 
-			git-r3_fetch "${subrepos[*]}" "${commit}" "${local_id}/${subname}"
+				git-r3_fetch "${subrepos[*]}" "${commit}" "${local_id}/${subname}"
+			fi
 
 			submodules=( "${submodules[@]:3}" ) # shift
 		done
@@ -849,11 +856,16 @@
 			local subname=${submodules[0]}
 			local url=${submodules[1]}
 			local path=${submodules[2]}
-			local subrepos
-			_git-r3_set_subrepos "${url}" "${repos[@]}"
 
-			git-r3_checkout "${subrepos[*]}" "${out_dir}/${path}" \
-				"${local_id}/${subname}"
+			# use only submodules for which path does exist
+			# (this is in par with 'git submodule'), bug #551100
+			if [[ -d ${out_dir}/${path} ]]; then
+				local subrepos
+				_git-r3_set_subrepos "${url}" "${repos[@]}"
+
+				git-r3_checkout "${subrepos[*]}" "${out_dir}/${path}" \
+					"${local_id}/${subname}"
+			fi
 
 			submodules=( "${submodules[@]:3}" ) # shift
 		done