Some index internals refactoring

Again, laying groundwork for some index iterator changes, this
contains a bunch of code refactorings for index internals that
should make it easier down the line to add locking around index
modifications.  Also this removes the redundant prefix_position
function and fixes some potential memory leaks.

include/git2/index.h

@@ -77,7 +77,12 @@ typedef struct git_index_entry {
 #define GIT_IDXENTRY_VALID     (0x8000)
 #define GIT_IDXENTRY_STAGESHIFT 12
 
-#define GIT_IDXENTRY_STAGE(E) (((E)->flags & GIT_IDXENTRY_STAGEMASK) >> GIT_IDXENTRY_STAGESHIFT)
+#define GIT_IDXENTRY_STAGE(E) \
+	(((E)->flags & GIT_IDXENTRY_STAGEMASK) >> GIT_IDXENTRY_STAGESHIFT)
+
+#define GIT_IDXENTRY_STAGE_SET(E,S) do { \
+	(E)->flags = ((E)->flags & ~GIT_IDXENTRY_STAGEMASK) | \
+		(((S) & 0x03) << GIT_IDXENTRY_STAGESHIFT); } while (0)
 
 /**
  * Bitmasks for on-disk fields of `git_index_entry`'s `flags_extended`
@@ -327,12 +332,14 @@ GIT_EXTERN(size_t) git_index_entrycount(const git_index *index);
 
 /**
  * Clear the contents (all the entries) of an index object.
- * This clears the index object in memory; changes must be manually
- * written to disk for them to take effect.
+ *
+ * This clears the index object in memory; changes must be explicitly
+ * written to disk for them to take effect persistently.
  *
  * @param index an existing index object
+ * @return 0 on success, error code < 0 on failure
  */
-GIT_EXTERN(void) git_index_clear(git_index *index);
+GIT_EXTERN(int) git_index_clear(git_index *index);
 
 /**
  * Get a pointer to one of the entries in the index

src/checkout.c

@@ -277,19 +277,23 @@ static int checkout_action_wd_only(
 
 	/* check if item is tracked in the index but not in the checkout diff */
 	if (data->index != NULL) {
+		size_t pos;
+
+		error = git_index__find(
+			&pos, data->index, wd->path, 0, GIT_INDEX_STAGE_ANY);
+
 		if (wd->mode != GIT_FILEMODE_TREE) {
-			if (!(error = git_index_find(NULL, data->index, wd->path))) {
+			if (!error) { /* found by git_index__find call */
 				notify = GIT_CHECKOUT_NOTIFY_DIRTY;
 				remove = ((data->strategy & GIT_CHECKOUT_FORCE) != 0);
 			} else if (error != GIT_ENOTFOUND)
 				return error;
 			else
-				giterr_clear();
+				error = 0; /* git_index__find does not set error msg */
 		} else {
 			/* for tree entries, we have to see if there are any index
 			 * entries that are contained inside that tree
 			 */
-			size_t pos = git_index__prefix_position(data->index, wd->path);
 			const git_index_entry *e = git_index_get_byindex(data->index, pos);
 
 			if (e != NULL && data->diff->pfxcomp(e->path, wd->path) == 0) {

src/index.h

@@ -50,11 +50,13 @@ struct git_index_conflict_iterator {
 extern void git_index_entry__init_from_stat(
 	git_index_entry *entry, struct stat *st, bool trust_mode);
 
-extern size_t git_index__prefix_position(git_index *index, const char *path);
-
 extern int git_index_entry__cmp(const void *a, const void *b);
 extern int git_index_entry__cmp_icase(const void *a, const void *b);
 
+/* Search index for `path`, returning GIT_ENOTFOUND if it does not exist.
+ * `at_pos` is set to the position where it is or would be inserted.
+ * Pass `path_len` as strlen of path or 0 to call strlen internally.
+ */
 extern int git_index__find(
 	size_t *at_pos, git_index *index, const char *path, size_t path_len, int stage);
 

src/iterator.c

@@ -815,8 +815,10 @@ static int index_iterator__reset(
 	if (iterator__reset_range(self, start, end) < 0)
 		return -1;
 
-	ii->current = ii->base.start ?
-		git_index__prefix_position(ii->index, ii->base.start) : 0;
+	ii->current = 0;
+
+	if (ii->base.start)
+		git_index__find(&ii->current, ii->index, ii->base.start, 0, 0);
 
 	if ((ie = index_iterator__skip_conflicts(ii)) == NULL)
 		return 0;