thodg/libgit2

diff --git a/src/notes.c b/src/notes.c
index 84ad940..e84e6f7 100644
--- a/src/notes.c
+++ b/src/notes.c
@@ -12,50 +12,62 @@
 #include "config.h"
 #include "iterator.h"
 
-static int find_subtree(git_tree **subtree, const git_oid *root,
-			git_repository *repo, const char *target, int *fanout)
+static int find_subtree_in_current_level(git_tree **out, git_repository *repo, git_tree *parent, const char *annotated_object_sha, int fanout)
 {
-	int error;
 	unsigned int i;
-	git_tree *tree;
 	const git_tree_entry *entry;
 
-	*subtree = NULL;
-
-	error = git_tree_lookup(&tree, repo, root);
-	if (error < 0)
-		return error;
+	*out = NULL;
+	
+	if (parent == NULL)
+		return GIT_ENOTFOUND;
 
-	for (i=0; i<git_tree_entrycount(tree); i++) {
-		entry = git_tree_entry_byindex(tree, i);
+	for (i = 0; i < git_tree_entrycount(parent); i++) {
+		entry = git_tree_entry_byindex(parent, i);
 
 		if (!git__ishex(git_tree_entry_name(entry)))
 			continue;
 
-		/*
-		 * A notes tree follows a strict byte-based progressive fanout
-		 * (i.e. using 2/38, 2/2/36, etc. fanouts, not e.g. 4/36 fanout)
-		 */
-
 		if (S_ISDIR(git_tree_entry_attributes(entry))
-			&& strlen(git_tree_entry_name(entry)) == 2
-			&& !strncmp(git_tree_entry_name(entry), target + *fanout, 2)) {
+			&& strlen(git_tree_entry_name(entry)) == 2 
+			&& !strncmp(git_tree_entry_name(entry), annotated_object_sha + fanout, 2))
+			return git_tree_lookup(out, repo, git_tree_entry_id(entry));
 
-			/* found matching subtree - unpack and resume lookup */
+		/* Not a DIR, so do we have an already existing blob? */
+		if (!strcmp(git_tree_entry_name(entry), annotated_object_sha + fanout))				
+			return GIT_EEXISTS;
+	}
 
-			git_oid subtree_sha;
-			git_oid_cpy(&subtree_sha, git_tree_entry_id(entry));
-			git_tree_free(tree);
+	return GIT_ENOTFOUND;
+}
 
-			*fanout += 2;
+static int find_subtree_r(git_tree **out, git_tree *root,
+			git_repository *repo, const char *target, int *fanout)
+{
+	int error;
+	git_tree *subtree = NULL;
 
-			return find_subtree(subtree, &subtree_sha, repo,
-					    target, fanout);
-		}
+	*out = NULL;
+
+	error = find_subtree_in_current_level(&subtree, repo, root, target, *fanout);
+	if (error == GIT_EEXISTS)
+	{
+		error = git_tree_lookup(out, repo, git_object_id((const git_object *)root));
+		goto cleanup;
 	}
 
-	*subtree = tree;
-	return 0;
+	if (error < 0)
+		goto cleanup;
+
+	*fanout += 2;
+	error = find_subtree_r(out, subtree, repo, target, fanout);
+
+	// *root is not ours to free, and the last subtree is the one being returned => we only need to free the subtrees in-between
+	if (*out != subtree)
+		git_tree_free(subtree);
+
+cleanup:
+	return error;
 }
 
 static int find_blob(git_oid *blob, git_tree *tree, const char *target)
@@ -76,191 +88,201 @@ static int find_blob(git_oid *blob, git_tree *tree, const char *target)
 	return GIT_ENOTFOUND;
 }
 
-static int note_write(git_oid *out, git_repository *repo,
-		      git_signature *author, git_signature *committer,
-		      const char *notes_ref, const char *note,
-		      const git_oid *tree_sha, const char *target,
-		      int nparents, git_commit **parents)
+static int tree_write(git_tree **out, git_repository *repo, git_tree *source_tree, const git_oid *object_oid, const char *treeentry_name, unsigned int attributes)
 {
-	int error, fanout = 0;
-	git_oid oid;
-	git_tree *tree = NULL;
+	int error;
+	git_treebuilder *tb = NULL;
 	git_tree_entry *entry;
-	git_treebuilder *tb;
-
-	/* check for existing notes tree */
-
-	if (tree_sha) {
-		error = find_subtree(&tree, tree_sha, repo, target, &fanout);
-		if (error < 0)
-			return error;
-
-		error = find_blob(&oid, tree, target + fanout);
-		if (error != GIT_ENOTFOUND) {
-			git_tree_free(tree);
-			if (!error) {
-				giterr_set(GITERR_REPOSITORY, "Note for '%s' exists already", target);
-				error = GIT_EEXISTS;
-			}
-			return error;
-		}
-	}
+	git_oid tree_oid;
 
-	/* no matching tree entry - add note object to target tree */
+	if ((error = git_treebuilder_create(&tb, source_tree)) < 0)
+		goto cleanup;
 
-	error = git_treebuilder_create(&tb, tree);
-	git_tree_free(tree);
+	if (object_oid) {
+		if ((error = git_treebuilder_insert(&entry, tb, treeentry_name, object_oid, attributes)) < 0)
+			goto cleanup;
+	} else {
+		if ((error = git_treebuilder_remove(tb, treeentry_name)) < 0)
+			goto cleanup;
+	}
 
-	if (error < 0)
-		return error;
+	if ((error = git_treebuilder_write(&tree_oid, repo, tb)) < 0)
+		goto cleanup;
 
-	if (!tree_sha)
-		/* no notes tree yet - create fanout */
-		fanout += 2;
+	error = git_tree_lookup(out, repo, &tree_oid);
 
-	/* create note object */
-	error = git_blob_create_frombuffer(&oid, repo, note, strlen(note));
-	if (error < 0) {
-		git_treebuilder_free(tb);
-		return error;
-	}
+cleanup:
+	git_treebuilder_free(tb);
+	return error;
+}
 
-	error = git_treebuilder_insert(&entry, tb, target + fanout, &oid, 0100644);
-	if (error < 0) {
-		/* libgit2 doesn't support object removal (gc) yet */
-		/* we leave an orphaned blob object behind - TODO */
+static int manipulate_note_in_tree_r(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, 
+	int (*note_exists_cb)(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error),
+	int (*note_notfound_cb)(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error))
+{
+	int error = -1;	
+	git_tree *subtree = NULL;
+	char subtree_name[3];
 
-		git_treebuilder_free(tb);
-		return error;
-	}
+	error = find_subtree_in_current_level(&subtree, repo, parent, annotated_object_sha, fanout);
 
-	if (out)
-		git_oid_cpy(out, git_tree_entry_id(entry));
+	if (error == GIT_EEXISTS) {
+		error = note_exists_cb(out, repo, parent, note_oid, annotated_object_sha, fanout, error);
+		goto cleanup;
+	}
 
-	error = git_treebuilder_write(&oid, repo, tb);
-	git_treebuilder_free(tb);
+	if (error == GIT_ENOTFOUND) {
+		error = note_notfound_cb(out, repo, parent, note_oid, annotated_object_sha, fanout, error);
+		goto cleanup;
+	}
 
 	if (error < 0)
-		return 0;
+		goto cleanup;
 
-	if (!tree_sha) {
-		/* create fanout subtree */
+	/* An existing fanout has been found, let's dig deeper */
+	error = manipulate_note_in_tree_r(out, repo, subtree, note_oid, annotated_object_sha, fanout + 2, note_exists_cb, note_notfound_cb);
+	if (error < 0)
+		goto cleanup;
 
-		char subtree[3];
-		strncpy(subtree, target, 2);
-		subtree[2] = '\0';
+	strncpy(subtree_name, annotated_object_sha + fanout, 2);
+	subtree_name[2] = '\0';
 
-		error = git_treebuilder_create(&tb, NULL);
-		if (error < 0)
-			return error;
+	error = tree_write(out, repo, parent, git_object_id((const git_object *)(*out)), subtree_name, 0040000);
 
-		error = git_treebuilder_insert(NULL, tb, subtree, &oid, 0040000);
-		if (error < 0) {
-			git_treebuilder_free(tb);
-			return error;
-		}
+cleanup:
+	git_tree_free(subtree);
+	return error;
+}
 
-		error = git_treebuilder_write(&oid, repo, tb);
+static int remove_note_in_tree_eexists_cb(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error) {
+	GIT_UNUSED(note_oid);
+	GIT_UNUSED(current_error);
 
-		git_treebuilder_free(tb);
+	return tree_write(out, repo, parent, NULL, annotated_object_sha + fanout, 0);
+}
 
-		if (error < 0)
-			return error;
-	}
+static int remove_note_in_tree_enotfound_cb(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error) {
+	GIT_UNUSED(out);
+	GIT_UNUSED(repo);
+	GIT_UNUSED(parent);
+	GIT_UNUSED(note_oid);
+	GIT_UNUSED(fanout);
 
-	/* create new notes commit */
+	giterr_set(GITERR_REPOSITORY, "Object '%s' has no note", annotated_object_sha);
+	return current_error;
+}
 
-	error = git_tree_lookup(&tree, repo, &oid);
-	if (error < 0)
-		return error;
+static int insert_note_in_tree_eexists_cb(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error) {
+	GIT_UNUSED(out);
+	GIT_UNUSED(repo);
+	GIT_UNUSED(parent);
+	GIT_UNUSED(note_oid);
+	GIT_UNUSED(fanout);
 
-	error = git_commit_create(&oid, repo, notes_ref, author, committer,
-				  NULL, GIT_NOTES_DEFAULT_MSG_ADD,
-				  tree, nparents, (const git_commit **) parents);
+	giterr_set(GITERR_REPOSITORY, "Note for '%s' exists already", annotated_object_sha);
+	return current_error;
+}
 
-	git_tree_free(tree);
+static int insert_note_in_tree_enotfound_cb(git_tree **out, git_repository *repo, git_tree *parent, git_oid *note_oid, const char *annotated_object_sha, int fanout, int current_error) {
+	GIT_UNUSED(current_error);
 
-	return error;
+	/* No existing fanout at this level, insert in place */
+	return tree_write(out, repo, parent, note_oid, annotated_object_sha + fanout, 0100644);
 }
 
-static int note_lookup(git_note **out, git_repository *repo,
-		       const git_oid *tree_sha, const char *target)
+static int note_write(git_oid *out, git_repository *repo,
+		      git_signature *author, git_signature *committer,
+		      const char *notes_ref, const char *note,
+		      git_tree *commit_tree, const char *target,
+		      git_commit **parents)
 {
-	int error, fanout = 0;
+	int error;
 	git_oid oid;
-	git_blob *blob;
-	git_tree *tree;
-	git_note *note;
+	git_tree *tree = NULL;
+	
+	// TODO: should we apply filters?
+	/* create note object */
+	if ((error = git_blob_create_frombuffer(&oid, repo, note, strlen(note))) < 0)
+		goto cleanup;
 
-	error = find_subtree(&tree, tree_sha, repo, target, &fanout);
-	if (error < 0)
-		return error;
+	if ((error = manipulate_note_in_tree_r(&tree, repo, commit_tree, &oid, target, 0, insert_note_in_tree_eexists_cb, insert_note_in_tree_enotfound_cb)) < 0)
+		goto cleanup;
 
-	error = find_blob(&oid, tree, target + fanout);
+	if (out)
+		git_oid_cpy(out, &oid);
 
+	error = git_commit_create(&oid, repo, notes_ref, author, committer,
+				  NULL, GIT_NOTES_DEFAULT_MSG_ADD,
+				  tree, *parents == NULL ? 0 : 1, (const git_commit **) parents);
+
+cleanup:
 	git_tree_free(tree);
-	if (error < 0)
-		return error;
+	return error;
+}
 
-	error = git_blob_lookup(&blob, repo, &oid);
-	if (error < 0)
-		return error;
+static int note_new(git_note **out, git_oid *note_oid, git_blob *blob)
+{
+	git_note *note = NULL;
 
-	note = git__malloc(sizeof(git_note));
+	note = (git_note *)git__malloc(sizeof(git_note));
 	GITERR_CHECK_ALLOC(note);
 
-	git_oid_cpy(&note->oid, &oid);
-	note->message = git__strdup(git_blob_rawcontent(blob));
+	git_oid_cpy(&note->oid, note_oid);
+	note->message = git__strdup((char *)git_blob_rawcontent(blob));
 	GITERR_CHECK_ALLOC(note->message);
 
 	*out = note;
 
-	git_blob_free(blob);
-	return error;
+	return 0;
 }
 
-static int note_remove(git_repository *repo,
-		       git_signature *author, git_signature *committer,
-		       const char *notes_ref, const git_oid *tree_sha,
-		       const char *target, int nparents, git_commit **parents)
+static int note_lookup(git_note **out, git_repository *repo,
+		       git_tree *tree, const char *target)
 {
 	int error, fanout = 0;
 	git_oid oid;
-	git_tree *tree;
-	git_treebuilder *tb;
+	git_blob *blob = NULL;
+	git_note *note = NULL;
+	git_tree *subtree = NULL;
 
-	error = find_subtree(&tree, tree_sha, repo, target, &fanout);
-	if (error < 0)
-		return error;
+	if ((error = find_subtree_r(&subtree, tree, repo, target, &fanout)) < 0)
+		goto cleanup;
 
-	error = find_blob(&oid, tree, target + fanout);
-	if (!error)
-		error = git_treebuilder_create(&tb, tree);
+	if ((error = find_blob(&oid, subtree, target + fanout)) < 0)
+		goto cleanup;
 
-	git_tree_free(tree);
-	if (error < 0)
-		return error;
+	if ((error = git_blob_lookup(&blob, repo, &oid)) < 0)
+		goto cleanup;
 
-	error = git_treebuilder_remove(tb, target + fanout);
-	if (!error)
-		error = git_treebuilder_write(&oid, repo, tb);
+	if ((error = note_new(&note, &oid, blob)) < 0)
+		goto cleanup;
 
-	git_treebuilder_free(tb);
-	if (error < 0)
-		return error;
+	*out = note;
 
-	/* create new notes commit */
+cleanup:
+	git_tree_free(subtree);
+	git_blob_free(blob);
+	return error;
+}
 
-	error = git_tree_lookup(&tree, repo, &oid);
-	if (error < 0)
-		return error;
+static int note_remove(git_repository *repo,
+		       git_signature *author, git_signature *committer,
+		       const char *notes_ref, git_tree *tree,
+		       const char *target, git_commit **parents)
+{
+	int error;
+	git_tree *tree_after_removal = NULL;
+	git_oid oid;
+		
+	if ((error = manipulate_note_in_tree_r(&tree_after_removal, repo, tree, NULL, target, 0, remove_note_in_tree_eexists_cb, remove_note_in_tree_enotfound_cb)) < 0)
+		goto cleanup;
 
 	error = git_commit_create(&oid, repo, notes_ref, author, committer,
 				  NULL, GIT_NOTES_DEFAULT_MSG_RM,
-				  tree, nparents, (const git_commit **) parents);
-
-	git_tree_free(tree);
+				  tree_after_removal, *parents == NULL ? 0 : 1, (const git_commit **) parents);
 
+cleanup:
+	git_tree_free(tree_after_removal);
 	return error;
 }
 
@@ -291,48 +313,46 @@ static int normalize_namespace(const char **notes_ref, git_repository *repo)
 	return note_get_default_ref(notes_ref, repo);
 }
 
-static int retrieve_note_tree_oid(git_oid *tree_oid_out, git_repository *repo, const char *notes_ref)
+static int retrieve_note_tree_and_commit(git_tree **tree_out, git_commit **commit_out, git_repository *repo, const char **notes_ref)
 {
-	int error = -1;
-	git_commit *commit = NULL;
+	int error;
 	git_oid oid;
 
-	if ((error = git_reference_name_to_oid(&oid, repo, notes_ref)) < 0)
-		goto cleanup;
+	if ((error = normalize_namespace(notes_ref, repo)) < 0)
+		return error;
 
-	if (git_commit_lookup(&commit, repo, &oid) < 0)
-		goto cleanup;
+	if ((error = git_reference_name_to_oid(&oid, repo, *notes_ref)) < 0)
+		return error;
 
-	git_oid_cpy(tree_oid_out, git_commit_tree_oid(commit));
+	if (git_commit_lookup(commit_out, repo, &oid) < 0)
+		return error;
 
-	error = 0;
+	if ((error = git_commit_tree(tree_out, *commit_out)) < 0)
+		return error;
 
-cleanup:
-	git_commit_free(commit);
-	return error;
+	return 0;
 }
 
 int git_note_read(git_note **out, git_repository *repo,
 		  const char *notes_ref, const git_oid *oid)
 {
 	int error;
-	char *target;
-	git_oid sha;
-
-	*out = NULL;
-
-	if (normalize_namespace(&notes_ref, repo) < 0)
-		return -1;
-
-	if ((error = retrieve_note_tree_oid(&sha, repo, notes_ref)) < 0)
-		return error;
+	char *target = NULL;
+	git_tree *tree = NULL;
+	git_commit *commit = NULL;
 
 	target = git_oid_allocfmt(oid);
 	GITERR_CHECK_ALLOC(target);
 
-	error = note_lookup(out, repo, &sha, target);
+	if ((error = retrieve_note_tree_and_commit(&tree, &commit, repo, &notes_ref)) < 0)
+		goto cleanup;
+
+	error = note_lookup(out, repo, tree, target);
 
+cleanup:
 	git__free(target);
+	git_tree_free(tree);
+	git_commit_free(commit);
 	return error;
 }
 
@@ -342,44 +362,26 @@ int git_note_create(
 	const char *notes_ref, const git_oid *oid,
 	const char *note)
 {
-	int error, nparents = 0;
-	char *target;
-	git_oid sha;
+	int error;
+	char *target = NULL;
 	git_commit *commit = NULL;
-	git_reference *ref;
-
-	if (normalize_namespace(&notes_ref, repo) < 0)
-		return -1;
-
-	error = git_reference_lookup(&ref, repo, notes_ref);
-	if (error < 0 && error != GIT_ENOTFOUND)
-		return error;
-
-	if (!error) {
-		assert(git_reference_type(ref) == GIT_REF_OID);
-
-		/* lookup existing notes tree oid */
-
-		git_oid_cpy(&sha, git_reference_oid(ref));
-		git_reference_free(ref);
-
-		error = git_commit_lookup(&commit, repo, &sha);
-		if (error < 0)
-			return error;
-
-		git_oid_cpy(&sha, git_commit_tree_oid(commit));
-		nparents++;
-	}
+	git_tree *tree = NULL;
 
 	target = git_oid_allocfmt(oid);
 	GITERR_CHECK_ALLOC(target);
 
+	error = retrieve_note_tree_and_commit(&tree, &commit, repo, &notes_ref);
+
+	if (error < 0 && error != GIT_ENOTFOUND)
+		goto cleanup;
+
 	error = note_write(out, repo, author, committer, notes_ref,
-			   note, nparents ? &sha : NULL, target,
-			   nparents, &commit);
+			   note, tree, target, &commit);
 
+cleanup:
 	git__free(target);
 	git_commit_free(commit);
+	git_tree_free(tree);
 	return error;
 }
 
@@ -388,37 +390,23 @@ int git_note_remove(git_repository *repo, const char *notes_ref,
 		    const git_oid *oid)
 {
 	int error;
-	char *target;
-	git_oid sha;
-	git_commit *commit;
-	git_reference *ref;
-
-	if (normalize_namespace(&notes_ref, repo) < 0)
-		return -1;
-
-	error = git_reference_lookup(&ref, repo, notes_ref);
-	if (error < 0)
-		return error;
-
-	assert(git_reference_type(ref) == GIT_REF_OID);
-
-	git_oid_cpy(&sha, git_reference_oid(ref));
-	git_reference_free(ref);
-
-	error = git_commit_lookup(&commit, repo, &sha);
-	if (error < 0)
-		return error;
-
-	git_oid_cpy(&sha, git_commit_tree_oid(commit));
+	char *target = NULL;
+	git_commit *commit = NULL;
+	git_tree *tree = NULL;
 
 	target = git_oid_allocfmt(oid);
 	GITERR_CHECK_ALLOC(target);
 
+	if ((error = retrieve_note_tree_and_commit(&tree, &commit, repo, &notes_ref)) < 0)
+		goto cleanup;
+
 	error = note_remove(repo, author, committer, notes_ref,
-			    &sha, target, 1, &commit);
+			    tree, target, &commit);
 
+cleanup:
 	git__free(target);
 	git_commit_free(commit);
+	git_tree_free(tree);
 	return error;
 }
 
@@ -511,18 +499,12 @@ int git_note_foreach(
 	void *payload)
 {
 	int error = -1;
-	git_oid tree_oid;
 	git_iterator *iter = NULL;
 	git_tree *tree = NULL;
+	git_commit *commit = NULL;
 	const git_index_entry *item;
 
-	if (normalize_namespace(&notes_ref, repo) < 0)
-		return -1;
-
-	if ((error = retrieve_note_tree_oid(&tree_oid, repo, notes_ref)) < 0)
-		goto cleanup;
-
-	if (git_tree_lookup(&tree, repo, &tree_oid) < 0)
+	if ((error = retrieve_note_tree_and_commit(&tree, &commit, repo, &notes_ref)) < 0)
 		goto cleanup;
 
 	if (git_iterator_for_tree(&iter, repo, tree) < 0)
@@ -544,5 +526,6 @@ int git_note_foreach(
 cleanup:
 	git_iterator_free(iter);
 	git_tree_free(tree);
+	git_commit_free(commit);
 	return error;
 }
diff --git a/tests-clar/notes/notes.c b/tests-clar/notes/notes.c
index d79c211..068e44c 100644
--- a/tests-clar/notes/notes.c
+++ b/tests-clar/notes/notes.c
@@ -179,3 +179,36 @@ void test_notes_notes__can_correctly_insert_a_note_in_an_existing_fanout(void)
 		git_oid_cpy(&target_oid, &note_oid);
 	}
 }
+
+/*
+ * $ git notes --ref fanout list 8496071c1b46c854b31185ea97743be6a8774479
+ * 08b041783f40edfe12bb406c9c9a8a040177c125
+ */
+void test_notes_notes__can_read_a_note_in_an_existing_fanout(void)
+{
+	git_oid note_oid, target_oid;
+	git_note *note;
+
+	cl_git_pass(git_oid_fromstr(&target_oid, "8496071c1b46c854b31185ea97743be6a8774479"));
+	cl_git_pass(git_note_read(&note, _repo, "refs/notes/fanout", &target_oid));
+
+	cl_git_pass(git_oid_fromstr(&note_oid, "08b041783f40edfe12bb406c9c9a8a040177c125"));
+	cl_assert(!git_oid_cmp(git_note_oid(note), &note_oid));
+
+	git_note_free(note);
+}
+
+/*
+ * $ git notes --ref fanout list 8496071c1b46c854b31185ea97743be6a8774479
+ * 08b041783f40edfe12bb406c9c9a8a040177c125
+ */
+void test_notes_notes__can_remove_a_note_in_an_existing_fanout(void)
+{
+	git_oid target_oid;
+	git_note *note;
+
+	cl_git_pass(git_oid_fromstr(&target_oid, "8496071c1b46c854b31185ea97743be6a8774479"));
+	cl_git_pass(git_note_remove(_repo, "refs/notes/fanout", _sig, _sig, &target_oid));
+
+	cl_git_fail(git_note_read(&note, _repo, "refs/notes/fanout", &target_oid));
+}