Merge branch 'mh/packed-refs-various'

Update reading and updating packed-refs file, correcting corner case
bugs.

* mh/packed-refs-various: (33 commits)
  refs: handle the main ref_cache specially
  refs: change do_for_each_*() functions to take ref_cache arguments
  pack_one_ref(): do some cheap tests before a more expensive one
  pack_one_ref(): use write_packed_entry() to do the writing
  pack_one_ref(): use function peel_entry()
  refs: inline function do_not_prune()
  pack_refs(): change to use do_for_each_entry()
  refs: use same lock_file object for both ref-packing functions
  pack_one_ref(): rename "path" parameter to "refname"
  pack-refs: merge code from pack-refs.{c,h} into refs.{c,h}
  pack-refs: rename handle_one_ref() to pack_one_ref()
  refs: extract a function write_packed_entry()
  repack_without_ref(): write peeled refs in the rewritten file
  t3211: demonstrate loss of peeled refs if a packed ref is deleted
  refs: change how packed refs are deleted
  search_ref_dir(): return an index rather than a pointer
  repack_without_ref(): silence errors for dangling packed refs
  t3210: test for spurious error messages for dangling packed refs
  refs: change the internal reference-iteration API
  refs: extract a function peel_entry()
  ...

9 files changed, 640 insertions, 341 deletions

diff --git a/Makefile b/Makefile
index 5f424a7e19..77f3f117c4 100644
--- a/Makefile
+++ b/Makefile
@@ -685,7 +685,6 @@ LIB_H += notes-cache.h
 LIB_H += notes-merge.h
 LIB_H += notes.h
 LIB_H += object.h
-LIB_H += pack-refs.h
 LIB_H += pack-revindex.h
 LIB_H += pack.h
 LIB_H += parse-options.h
@@ -818,7 +817,6 @@ LIB_OBJS += notes-cache.o
 LIB_OBJS += notes-merge.o
 LIB_OBJS += object.o
 LIB_OBJS += pack-check.o
-LIB_OBJS += pack-refs.o
 LIB_OBJS += pack-revindex.o
 LIB_OBJS += pack-write.o
 LIB_OBJS += pager.o
diff --git a/builtin/clone.c b/builtin/clone.c
index 035ab64950..5e70696d84 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -18,7 +18,6 @@
 #include "transport.h"
 #include "strbuf.h"
 #include "dir.h"
-#include "pack-refs.h"
 #include "sigchain.h"
 #include "branch.h"
 #include "remote.h"
diff --git a/builtin/pack-refs.c b/builtin/pack-refs.c
index b5a0f88eb8..b20b1ec4c1 100644
--- a/builtin/pack-refs.c
+++ b/builtin/pack-refs.c
@@ -1,6 +1,6 @@
 #include "builtin.h"
 #include "parse-options.h"
-#include "pack-refs.h"
+#include "refs.h"
 
 static char const * const pack_refs_usage[] = {
 	N_("git pack-refs [options]"),
diff --git a/pack-refs.c b/pack-refs.c
deleted file mode 100644
index 4461f71a37..0000000000
--- a/pack-refs.c
+++ /dev/null
@@ -1,148 +0,0 @@
-#include "cache.h"
-#include "refs.h"
-#include "tag.h"
-#include "pack-refs.h"
-
-struct ref_to_prune {
-	struct ref_to_prune *next;
-	unsigned char sha1[20];
-	char name[FLEX_ARRAY];
-};
-
-struct pack_refs_cb_data {
-	unsigned int flags;
-	struct ref_to_prune *ref_to_prune;
-	FILE *refs_file;
-};
-
-static int do_not_prune(int flags)
-{
-	/* If it is already packed or if it is a symref,
-	 * do not prune it.
-	 */
-	return (flags & (REF_ISSYMREF|REF_ISPACKED));
-}
-
-static int handle_one_ref(const char *path, const unsigned char *sha1,
-			  int flags, void *cb_data)
-{
-	struct pack_refs_cb_data *cb = cb_data;
-	struct object *o;
-	int is_tag_ref;
-
-	/* Do not pack the symbolic refs */
-	if ((flags & REF_ISSYMREF))
-		return 0;
-	is_tag_ref = !prefixcmp(path, "refs/tags/");
-
-	/* ALWAYS pack refs that were already packed or are tags */
-	if (!(cb->flags & PACK_REFS_ALL) && !is_tag_ref && !(flags & REF_ISPACKED))
-		return 0;
-
-	fprintf(cb->refs_file, "%s %s\n", sha1_to_hex(sha1), path);
-
-	o = parse_object_or_die(sha1, path);
-	if (o->type == OBJ_TAG) {
-		o = deref_tag(o, path, 0);
-		if (o)
-			fprintf(cb->refs_file, "^%s\n",
-				sha1_to_hex(o->sha1));
-	}
-
-	if ((cb->flags & PACK_REFS_PRUNE) && !do_not_prune(flags)) {
-		int namelen = strlen(path) + 1;
-		struct ref_to_prune *n = xcalloc(1, sizeof(*n) + namelen);
-		hashcpy(n->sha1, sha1);
-		strcpy(n->name, path);
-		n->next = cb->ref_to_prune;
-		cb->ref_to_prune = n;
-	}
-	return 0;
-}
-
-/*
- * Remove empty parents, but spare refs/ and immediate subdirs.
- * Note: munges *name.
- */
-static void try_remove_empty_parents(char *name)
-{
-	char *p, *q;
-	int i;
-	p = name;
-	for (i = 0; i < 2; i++) { /* refs/{heads,tags,...}/ */
-		while (*p && *p != '/')
-			p++;
-		/* tolerate duplicate slashes; see check_refname_format() */
-		while (*p == '/')
-			p++;
-	}
-	for (q = p; *q; q++)
-		;
-	while (1) {
-		while (q > p && *q != '/')
-			q--;
-		while (q > p && *(q-1) == '/')
-			q--;
-		if (q == p)
-			break;
-		*q = '\0';
-		if (rmdir(git_path("%s", name)))
-			break;
-	}
-}
-
-/* make sure nobody touched the ref, and unlink */
-static void prune_ref(struct ref_to_prune *r)
-{
-	struct ref_lock *lock = lock_ref_sha1(r->name + 5, r->sha1);
-
-	if (lock) {
-		unlink_or_warn(git_path("%s", r->name));
-		unlock_ref(lock);
-		try_remove_empty_parents(r->name);
-	}
-}
-
-static void prune_refs(struct ref_to_prune *r)
-{
-	while (r) {
-		prune_ref(r);
-		r = r->next;
-	}
-}
-
-static struct lock_file packed;
-
-int pack_refs(unsigned int flags)
-{
-	int fd;
-	struct pack_refs_cb_data cbdata;
-
-	memset(&cbdata, 0, sizeof(cbdata));
-	cbdata.flags = flags;
-
-	fd = hold_lock_file_for_update(&packed, git_path("packed-refs"),
-				       LOCK_DIE_ON_ERROR);
-	cbdata.refs_file = fdopen(fd, "w");
-	if (!cbdata.refs_file)
-		die_errno("unable to create ref-pack file structure");
-
-	/* perhaps other traits later as well */
-	fprintf(cbdata.refs_file, "# pack-refs with: peeled fully-peeled \n");
-
-	for_each_ref(handle_one_ref, &cbdata);
-	if (ferror(cbdata.refs_file))
-		die("failed to write ref-pack file");
-	if (fflush(cbdata.refs_file) || fsync(fd) || fclose(cbdata.refs_file))
-		die_errno("failed to write ref-pack file");
-	/*
-	 * Since the lock file was fdopen()'ed and then fclose()'ed above,
-	 * assign -1 to the lock file descriptor so that commit_lock_file()
-	 * won't try to close() it.
-	 */
-	packed.fd = -1;
-	if (commit_lock_file(&packed) < 0)
-		die_errno("unable to overwrite old ref-pack file");
-	prune_refs(cbdata.ref_to_prune);
-	return 0;
-}
diff --git a/pack-refs.h b/pack-refs.h
deleted file mode 100644
index 518acfb370..0000000000
--- a/pack-refs.h
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef PACK_REFS_H
-#define PACK_REFS_H
-
-/*
- * Flags for controlling behaviour of pack_refs()
- * PACK_REFS_PRUNE: Prune loose refs after packing
- * PACK_REFS_ALL:   Pack _all_ refs, not just tags and already packed refs
- */
-#define PACK_REFS_PRUNE 0x0001
-#define PACK_REFS_ALL   0x0002
-
-/*
- * Write a packed-refs file for the current repository.
- * flags: Combination of the above PACK_REFS_* flags.
- */
-int pack_refs(unsigned int flags);
-
-#endif /* PACK_REFS_H */
diff --git a/refs.c b/refs.c
index de2d8eb866..d17931a8bc 100644
--- a/refs.c
+++ b/refs.c
@@ -109,7 +109,20 @@ struct ref_entry;
  * (ref_entry->flag & REF_DIR) is zero.
  */
 struct ref_value {
+	/*
+	 * The name of the object to which this reference resolves
+	 * (which may be a tag object).  If REF_ISBROKEN, this is
+	 * null.  If REF_ISSYMREF, then this is the name of the object
+	 * referred to by the last reference in the symlink chain.
+	 */
 	unsigned char sha1[20];
+
+	/*
+	 * If REF_KNOWS_PEELED, then this field holds the peeled value
+	 * of this reference, or null if the reference is known not to
+	 * be peelable.  See the documentation for peel_ref() for an
+	 * exact definition of "peelable".
+	 */
 	unsigned char peeled[20];
 };
 
@@ -158,7 +171,17 @@ struct ref_dir {
 	struct ref_entry **entries;
 };
 
-/* ISSYMREF=0x01, ISPACKED=0x02, and ISBROKEN=0x04 are public interfaces */
+/*
+ * Bit values for ref_entry::flag.  REF_ISSYMREF=0x01,
+ * REF_ISPACKED=0x02, and REF_ISBROKEN=0x04 are public values; see
+ * refs.h.
+ */
+
+/*
+ * The field ref_entry->u.value.peeled of this value entry contains
+ * the correct peeled value for the reference, which might be
+ * null_sha1 if the reference is not a tag or if it is broken.
+ */
 #define REF_KNOWS_PEELED 0x08
 
 /* ref_entry represents a directory of references */
@@ -343,18 +366,17 @@ static int ref_entry_cmp_sslice(const void *key_, const void *ent_)
 }
 
 /*
- * Return the entry with the given refname from the ref_dir
- * (non-recursively), sorting dir if necessary.  Return NULL if no
- * such entry is found.  dir must already be complete.
+ * Return the index of the entry with the given refname from the
+ * ref_dir (non-recursively), sorting dir if necessary.  Return -1 if
+ * no such entry is found.  dir must already be complete.
  */
-static struct ref_entry *search_ref_dir(struct ref_dir *dir,
-					const char *refname, size_t len)
+static int search_ref_dir(struct ref_dir *dir, const char *refname, size_t len)
 {
 	struct ref_entry **r;
 	struct string_slice key;
 
 	if (refname == NULL || !dir->nr)
-		return NULL;
+		return -1;
 
 	sort_ref_dir(dir);
 	key.len = len;
@@ -363,9 +385,9 @@ static struct ref_entry *search_ref_dir(struct ref_dir *dir,
 		    ref_entry_cmp_sslice);
 
 	if (r == NULL)
-		return NULL;
+		return -1;
 
-	return *r;
+	return r - dir->entries;
 }
 
 /*
@@ -379,8 +401,9 @@ static struct ref_dir *search_for_subdir(struct ref_dir *dir,
 					 const char *subdirname, size_t len,
 					 int mkdir)
 {
-	struct ref_entry *entry = search_ref_dir(dir, subdirname, len);
-	if (!entry) {
+	int entry_index = search_ref_dir(dir, subdirname, len);
+	struct ref_entry *entry;
+	if (entry_index == -1) {
 		if (!mkdir)
 			return NULL;
 		/*
@@ -391,6 +414,8 @@ static struct ref_dir *search_for_subdir(struct ref_dir *dir,
 		 */
 		entry = create_dir_entry(dir->ref_cache, subdirname, len, 0);
 		add_entry_to_dir(dir, entry);
+	} else {
+		entry = dir->entries[entry_index];
 	}
 	return get_ref_dir(entry);
 }
@@ -429,12 +454,67 @@ static struct ref_dir *find_containing_dir(struct ref_dir *dir,
  */
 static struct ref_entry *find_ref(struct ref_dir *dir, const char *refname)
 {
+	int entry_index;
 	struct ref_entry *entry;
 	dir = find_containing_dir(dir, refname, 0);
 	if (!dir)
 		return NULL;
-	entry = search_ref_dir(dir, refname, strlen(refname));
-	return (entry && !(entry->flag & REF_DIR)) ? entry : NULL;
+	entry_index = search_ref_dir(dir, refname, strlen(refname));
+	if (entry_index == -1)
+		return NULL;
+	entry = dir->entries[entry_index];
+	return (entry->flag & REF_DIR) ? NULL : entry;
+}
+
+/*
+ * Remove the entry with the given name from dir, recursing into
+ * subdirectories as necessary.  If refname is the name of a directory
+ * (i.e., ends with '/'), then remove the directory and its contents.
+ * If the removal was successful, return the number of entries
+ * remaining in the directory entry that contained the deleted entry.
+ * If the name was not found, return -1.  Please note that this
+ * function only deletes the entry from the cache; it does not delete
+ * it from the filesystem or ensure that other cache entries (which
+ * might be symbolic references to the removed entry) are updated.
+ * Nor does it remove any containing dir entries that might be made
+ * empty by the removal.  dir must represent the top-level directory
+ * and must already be complete.
+ */
+static int remove_entry(struct ref_dir *dir, const char *refname)
+{
+	int refname_len = strlen(refname);
+	int entry_index;
+	struct ref_entry *entry;
+	int is_dir = refname[refname_len - 1] == '/';
+	if (is_dir) {
+		/*
+		 * refname represents a reference directory.  Remove
+		 * the trailing slash; otherwise we will get the
+		 * directory *representing* refname rather than the
+		 * one *containing* it.
+		 */
+		char *dirname = xmemdupz(refname, refname_len - 1);
+		dir = find_containing_dir(dir, dirname, 0);
+		free(dirname);
+	} else {
+		dir = find_containing_dir(dir, refname, 0);
+	}
+	if (!dir)
+		return -1;
+	entry_index = search_ref_dir(dir, refname, refname_len);
+	if (entry_index == -1)
+		return -1;
+	entry = dir->entries[entry_index];
+
+	memmove(&dir->entries[entry_index],
+		&dir->entries[entry_index + 1],
+		(dir->nr - entry_index - 1) * sizeof(*dir->entries)
+		);
+	dir->nr--;
+	if (dir->sorted > entry_index)
+		dir->sorted--;
+	free_ref_entry(entry);
+	return dir->nr;
 }
 
 /*
@@ -503,27 +583,64 @@ static void sort_ref_dir(struct ref_dir *dir)
 	dir->sorted = dir->nr = i;
 }
 
-#define DO_FOR_EACH_INCLUDE_BROKEN 01
+/* Include broken references in a do_for_each_ref*() iteration: */
+#define DO_FOR_EACH_INCLUDE_BROKEN 0x01
+
+/*
+ * Return true iff the reference described by entry can be resolved to
+ * an object in the database.  Emit a warning if the referred-to
+ * object does not exist.
+ */
+static int ref_resolves_to_object(struct ref_entry *entry)
+{
+	if (entry->flag & REF_ISBROKEN)
+		return 0;
+	if (!has_sha1_file(entry->u.value.sha1)) {
+		error("%s does not point to a valid object!", entry->name);
+		return 0;
+	}
+	return 1;
+}
 
+/*
+ * current_ref is a performance hack: when iterating over references
+ * using the for_each_ref*() functions, current_ref is set to the
+ * current reference's entry before calling the callback function.  If
+ * the callback function calls peel_ref(), then peel_ref() first
+ * checks whether the reference to be peeled is the current reference
+ * (it usually is) and if so, returns that reference's peeled version
+ * if it is available.  This avoids a refname lookup in a common case.
+ */
 static struct ref_entry *current_ref;
 
-static int do_one_ref(const char *base, each_ref_fn fn, int trim,
-		      int flags, void *cb_data, struct ref_entry *entry)
+typedef int each_ref_entry_fn(struct ref_entry *entry, void *cb_data);
+
+struct ref_entry_cb {
+	const char *base;
+	int trim;
+	int flags;
+	each_ref_fn *fn;
+	void *cb_data;
+};
+
+/*
+ * Handle one reference in a do_for_each_ref*()-style iteration,
+ * calling an each_ref_fn for each entry.
+ */
+static int do_one_ref(struct ref_entry *entry, void *cb_data)
 {
+	struct ref_entry_cb *data = cb_data;
 	int retval;
-	if (prefixcmp(entry->name, base))
+	if (prefixcmp(entry->name, data->base))
+		return 0;
+
+	if (!(data->flags & DO_FOR_EACH_INCLUDE_BROKEN) &&
+	      !ref_resolves_to_object(entry))
 		return 0;
 
-	if (!(flags & DO_FOR_EACH_INCLUDE_BROKEN)) {
-		if (entry->flag & REF_ISBROKEN)
-			return 0; /* ignore broken refs e.g. dangling symref */
-		if (!has_sha1_file(entry->u.value.sha1)) {
-			error("%s does not point to a valid object!", entry->name);
-			return 0;
-		}
-	}
 	current_ref = entry;
-	retval = fn(entry->name + trim, entry->u.value.sha1, entry->flag, cb_data);
+	retval = data->fn(entry->name + data->trim, entry->u.value.sha1,
+			  entry->flag, data->cb_data);
 	current_ref = NULL;
 	return retval;
 }
@@ -532,11 +649,11 @@ static int do_one_ref(const char *base, each_ref_fn fn, int trim,
  * Call fn for each reference in dir that has index in the range
  * offset <= index < dir->nr.  Recurse into subdirectories that are in
  * that index range, sorting them before iterating.  This function
- * does not sort dir itself; it should be sorted beforehand.
+ * does not sort dir itself; it should be sorted beforehand.  fn is
+ * called for all references, including broken ones.
  */
-static int do_for_each_ref_in_dir(struct ref_dir *dir, int offset,
-				  const char *base,
-				  each_ref_fn fn, int trim, int flags, void *cb_data)
+static int do_for_each_entry_in_dir(struct ref_dir *dir, int offset,
+				    each_ref_entry_fn fn, void *cb_data)
 {
 	int i;
 	assert(dir->sorted == dir->nr);
@@ -546,10 +663,9 @@ static int do_for_each_ref_in_dir(struct ref_dir *dir, int offset,
 		if (entry->flag & REF_DIR) {
 			struct ref_dir *subdir = get_ref_dir(entry);
 			sort_ref_dir(subdir);
-			retval = do_for_each_ref_in_dir(subdir, 0,
-							base, fn, trim, flags, cb_data);
+			retval = do_for_each_entry_in_dir(subdir, 0, fn, cb_data);
 		} else {
-			retval = do_one_ref(base, fn, trim, flags, cb_data, entry);
+			retval = fn(entry, cb_data);
 		}
 		if (retval)
 			return retval;
@@ -562,12 +678,12 @@ static int do_for_each_ref_in_dir(struct ref_dir *dir, int offset,
  * by refname.  Recurse into subdirectories.  If a value entry appears
  * in both dir1 and dir2, then only process the version that is in
  * dir2.  The input dirs must already be sorted, but subdirs will be
- * sorted as needed.
+ * sorted as needed.  fn is called for all references, including
+ * broken ones.
  */
-static int do_for_each_ref_in_dirs(struct ref_dir *dir1,
-				   struct ref_dir *dir2,
-				   const char *base, each_ref_fn fn, int trim,
-				   int flags, void *cb_data)
+static int do_for_each_entry_in_dirs(struct ref_dir *dir1,
+				     struct ref_dir *dir2,
+				     each_ref_entry_fn fn, void *cb_data)
 {
 	int retval;
 	int i1 = 0, i2 = 0;
@@ -578,12 +694,10 @@ static int do_for_each_ref_in_dirs(struct ref_dir *dir1,
 		struct ref_entry *e1, *e2;
 		int cmp;
 		if (i1 == dir1->nr) {
-			return do_for_each_ref_in_dir(dir2, i2,
-						      base, fn, trim, flags, cb_data);
+			return do_for_each_entry_in_dir(dir2, i2, fn, cb_data);
 		}
 		if (i2 == dir2->nr) {
-			return do_for_each_ref_in_dir(dir1, i1,
-						      base, fn, trim, flags, cb_data);
+			return do_for_each_entry_in_dir(dir1, i1, fn, cb_data);
 		}
 		e1 = dir1->entries[i1];
 		e2 = dir2->entries[i2];
@@ -595,14 +709,13 @@ static int do_for_each_ref_in_dirs(struct ref_dir *dir1,
 				struct ref_dir *subdir2 = get_ref_dir(e2);
 				sort_ref_dir(subdir1);
 				sort_ref_dir(subdir2);
-				retval = do_for_each_ref_in_dirs(
-						subdir1, subdir2,
-						base, fn, trim, flags, cb_data);
+				retval = do_for_each_entry_in_dirs(
+						subdir1, subdir2, fn, cb_data);
 				i1++;
 				i2++;
 			} else if (!(e1->flag & REF_DIR) && !(e2->flag & REF_DIR)) {
 				/* Both are references; ignore the one from dir1. */
-				retval = do_one_ref(base, fn, trim, flags, cb_data, e2);
+				retval = fn(e2, cb_data);
 				i1++;
 				i2++;
 			} else {
@@ -621,23 +734,15 @@ static int do_for_each_ref_in_dirs(struct ref_dir *dir1,
 			if (e->flag & REF_DIR) {
 				struct ref_dir *subdir = get_ref_dir(e);
 				sort_ref_dir(subdir);
-				retval = do_for_each_ref_in_dir(
-						subdir, 0,
-						base, fn, trim, flags, cb_data);
+				retval = do_for_each_entry_in_dir(
+						subdir, 0, fn, cb_data);
 			} else {
-				retval = do_one_ref(base, fn, trim, flags, cb_data, e);
+				retval = fn(e, cb_data);
 			}
 		}
 		if (retval)
 			return retval;
 	}
-	if (i1 < dir1->nr)
-		return do_for_each_ref_in_dir(dir1, i1,
-					      base, fn, trim, flags, cb_data);
-	if (i2 < dir2->nr)
-		return do_for_each_ref_in_dir(dir2, i2,
-					      base, fn, trim, flags, cb_data);
-	return 0;
 }
 
 /*
@@ -661,14 +766,13 @@ struct name_conflict_cb {
 	const char *conflicting_refname;
 };
 
-static int name_conflict_fn(const char *existingrefname, const unsigned char *sha1,
-			    int flags, void *cb_data)
+static int name_conflict_fn(struct ref_entry *entry, void *cb_data)
 {
 	struct name_conflict_cb *data = (struct name_conflict_cb *)cb_data;
-	if (data->oldrefname && !strcmp(data->oldrefname, existingrefname))
+	if (data->oldrefname && !strcmp(data->oldrefname, entry->name))
 		return 0;
-	if (names_conflict(data->refname, existingrefname)) {
-		data->conflicting_refname = existingrefname;
+	if (names_conflict(data->refname, entry->name)) {
+		data->conflicting_refname = entry->name;
 		return 1;
 	}
 	return 0;
@@ -676,7 +780,7 @@ static int name_conflict_fn(const char *existingrefname, const unsigned char *sh
 
 /*
  * Return true iff a reference named refname could be created without
- * conflicting with the name of an existing reference in array.  If
+ * conflicting with the name of an existing reference in dir.  If
  * oldrefname is non-NULL, ignore potential conflicts with oldrefname
  * (e.g., because oldrefname is scheduled for deletion in the same
  * operation).
@@ -690,9 +794,7 @@ static int is_refname_available(const char *refname, const char *oldrefname,
 	data.conflicting_refname = NULL;
 
 	sort_ref_dir(dir);
-	if (do_for_each_ref_in_dir(dir, 0, "", name_conflict_fn,
-				   0, DO_FOR_EACH_INCLUDE_BROKEN,
-				   &data)) {
+	if (do_for_each_entry_in_dir(dir, 0, name_conflict_fn, &data)) {
 		error("'%s' exists; cannot create '%s'",
 		      data.conflicting_refname, refname);
 		return 0;
@@ -708,9 +810,13 @@ static struct ref_cache {
 	struct ref_cache *next;
 	struct ref_entry *loose;
 	struct ref_entry *packed;
-	/* The submodule name, or "" for the main repo. */
-	char name[FLEX_ARRAY];
-} *ref_cache;
+	/*
+	 * The submodule name, or "" for the main repo.  We allocate
+	 * length 1 rather than FLEX_ARRAY so that the main ref_cache
+	 * is initialized correctly.
+	 */
+	char name[1];
+} ref_cache, *submodule_ref_caches;
 
 static void clear_packed_ref_cache(struct ref_cache *refs)
 {
@@ -748,18 +854,18 @@ static struct ref_cache *create_ref_cache(const char *submodule)
  */
 static struct ref_cache *get_ref_cache(const char *submodule)
 {
-	struct ref_cache *refs = ref_cache;
-	if (!submodule)
-		submodule = "";
-	while (refs) {
+	struct ref_cache *refs;
+
+	if (!submodule || !*submodule)
+		return &ref_cache;
+
+	for (refs = submodule_ref_caches; refs; refs = refs->next)
 		if (!strcmp(submodule, refs->name))
 			return refs;
-		refs = refs->next;
-	}
 
 	refs = create_ref_cache(submodule);
-	refs->next = ref_cache;
-	ref_cache = refs;
+	refs->next = submodule_ref_caches;
+	submodule_ref_caches = refs;
 	return refs;
 }
 
@@ -770,6 +876,16 @@ void invalidate_ref_cache(const char *submodule)
 	clear_loose_ref_cache(refs);
 }
 
+/* The length of a peeled reference line in packed-refs, including EOL: */
+#define PEELED_LINE_LENGTH 42
+
+/*
+ * The packed-refs header line that we write out.  Perhaps other
+ * traits will be added later.  The trailing space is required.
+ */
+static const char PACKED_REFS_HEADER[] =
+	"# pack-refs with: peeled fully-peeled \n";
+
 /*
  * Parse one line from a packed-refs file.  Write the SHA1 to sha1.
  * Return a pointer to the refname within the line (null-terminated),
@@ -862,8 +978,8 @@ static void read_packed_refs(FILE *f, struct ref_dir *dir)
 		}
 		if (last &&
 		    refline[0] == '^' &&
-		    strlen(refline) == 42 &&
-		    refline[41] == '\n' &&
+		    strlen(refline) == PEELED_LINE_LENGTH &&
+		    refline[PEELED_LINE_LENGTH - 1] == '\n' &&
 		    !get_sha1_hex(refline + 1, sha1)) {
 			hashcpy(last->u.value.peeled, sha1);
 			/*
@@ -898,8 +1014,8 @@ static struct ref_dir *get_packed_refs(struct ref_cache *refs)
 
 void add_packed_ref(const char *refname, const unsigned char *sha1)
 {
-	add_ref(get_packed_refs(get_ref_cache(NULL)),
-			create_ref_entry(refname, sha1, REF_ISPACKED, 1));
+	add_ref(get_packed_refs(&ref_cache),
+		create_ref_entry(refname, sha1, REF_ISPACKED, 1));
 }
 
 /*
@@ -1069,18 +1185,12 @@ int resolve_gitlink_ref(const char *path, const char *refname, unsigned char *sh
 }
 
 /*
- * Try to read ref from the packed references.  On success, set sha1
- * and return 0; otherwise, return -1.
+ * Return the ref_entry for the given refname from the packed
+ * references.  If it does not exist, return NULL.
  */
-static int get_packed_ref(const char *refname, unsigned char *sha1)
+static struct ref_entry *get_packed_ref(const char *refname)
 {
-	struct ref_dir *packed = get_packed_refs(get_ref_cache(NULL));
-	struct ref_entry *entry = find_ref(packed, refname);
-	if (entry) {
-		hashcpy(sha1, entry->u.value.sha1);
-		return 0;
-	}
-	return -1;
+	return find_ref(get_packed_refs(&ref_cache), refname);
 }
 
 const char *resolve_ref_unsafe(const char *refname, unsigned char *sha1, int reading, int *flag)
@@ -1108,13 +1218,17 @@ const char *resolve_ref_unsafe(const char *refname, unsigned char *sha1, int rea
 		git_snpath(path, sizeof(path), "%s", refname);
 
 		if (lstat(path, &st) < 0) {
+			struct ref_entry *entry;
+
 			if (errno != ENOENT)
 				return NULL;
 			/*
 			 * The loose reference file does not exist;
 			 * check for a packed reference.
 			 */
-			if (!get_packed_ref(refname, sha1)) {
+			entry = get_packed_ref(refname);
+			if (entry) {
+				hashcpy(sha1, entry->u.value.sha1);
 				if (flag)
 					*flag |= REF_ISPACKED;
 				return refname;
@@ -1231,54 +1345,130 @@ static int filter_refs(const char *refname, const unsigned char *sha1, int flags
 	return filter->fn(refname, sha1, flags, filter->cb_data);
 }
 
+enum peel_status {
+	/* object was peeled successfully: */
+	PEEL_PEELED = 0,
+
+	/*
+	 * object cannot be peeled because the named object (or an
+	 * object referred to by a tag in the peel chain), does not
+	 * exist.
+	 */
+	PEEL_INVALID = -1,
+
+	/* object cannot be peeled because it is not a tag: */
+	PEEL_NON_TAG = -2,
+
+	/* ref_entry contains no peeled value because it is a symref: */
+	PEEL_IS_SYMREF = -3,
+
+	/*
+	 * ref_entry cannot be peeled because it is broken (i.e., the
+	 * symbolic reference cannot even be resolved to an object
+	 * name):
+	 */
+	PEEL_BROKEN = -4
+};
+
+/*
+ * Peel the named object; i.e., if the object is a tag, resolve the
+ * tag recursively until a non-tag is found.  If successful, store the
+ * result to sha1 and return PEEL_PEELED.  If the object is not a tag
+ * or is not valid, return PEEL_NON_TAG or PEEL_INVALID, respectively,
+ * and leave sha1 unchanged.
+ */
+static enum peel_status peel_object(const unsigned char *name, unsigned char *sha1)
+{
+	struct object *o = lookup_unknown_object(name);
+
+	if (o->type == OBJ_NONE) {
+		int type = sha1_object_info(name, NULL);
+		if (type < 0)
+			return PEEL_INVALID;
+		o->type = type;
+	}
+
+	if (o->type != OBJ_TAG)
+		return PEEL_NON_TAG;
+
+	o = deref_tag_noverify(o);
+	if (!o)
+		return PEEL_INVALID;
+
+	hashcpy(sha1, o->sha1);
+	return PEEL_PEELED;
+}
+
+/*
+ * Peel the entry (if possible) and return its new peel_status.  If
+ * repeel is true, re-peel the entry even if there is an old peeled
+ * value that is already stored in it.
+ *
+ * It is OK to call this function with a packed reference entry that
+ * might be stale and might even refer to an object that has since
+ * been garbage-collected.  In such a case, if the entry has
+ * REF_KNOWS_PEELED then leave the status unchanged and return
+ * PEEL_PEELED or PEEL_NON_TAG; otherwise, return PEEL_INVALID.
+ */
+static enum peel_status peel_entry(struct ref_entry *entry, int repeel)
+{
+	enum peel_status status;
+
+	if (entry->flag & REF_KNOWS_PEELED) {
+		if (repeel) {
+			entry->flag &= ~REF_KNOWS_PEELED;
+			hashclr(entry->u.value.peeled);
+		} else {
+			return is_null_sha1(entry->u.value.peeled) ?
+				PEEL_NON_TAG : PEEL_PEELED;
+		}
+	}
+	if (entry->flag & REF_ISBROKEN)
+		return PEEL_BROKEN;
+	if (entry->flag & REF_ISSYMREF)
+		return PEEL_IS_SYMREF;
+
+	status = peel_object(entry->u.value.sha1, entry->u.value.peeled);
+	if (status == PEEL_PEELED || status == PEEL_NON_TAG)
+		entry->flag |= REF_KNOWS_PEELED;
+	return status;
+}
+
 int peel_ref(const char *refname, unsigned char *sha1)
 {
 	int flag;
 	unsigned char base[20];
-	struct object *o;
 
 	if (current_ref && (current_ref->name == refname
-		|| !strcmp(current_ref->name, refname))) {
-		if (current_ref->flag & REF_KNOWS_PEELED) {
-			if (is_null_sha1(current_ref->u.value.peeled))
-			    return -1;
-			hashcpy(sha1, current_ref->u.value.peeled);
-			return 0;
-		}
-		hashcpy(base, current_ref->u.value.sha1);
-		goto fallback;
+			    || !strcmp(current_ref->name, refname))) {
+		if (peel_entry(current_ref, 0))
+			return -1;
+		hashcpy(sha1, current_ref->u.value.peeled);
+		return 0;
 	}
 
 	if (read_ref_full(refname, base, 1, &flag))
 		return -1;
 
-	if ((flag & REF_ISPACKED)) {
-		struct ref_dir *dir = get_packed_refs(get_ref_cache(NULL));
-		struct ref_entry *r = find_ref(dir, refname);
-
-		if (r != NULL && r->flag & REF_KNOWS_PEELED) {
+	/*
+	 * If the reference is packed, read its ref_entry from the
+	 * cache in the hope that we already know its peeled value.
+	 * We only try this optimization on packed references because
+	 * (a) forcing the filling of the loose reference cache could
+	 * be expensive and (b) loose references anyway usually do not
+	 * have REF_KNOWS_PEELED.
+	 */
+	if (flag & REF_ISPACKED) {
+		struct ref_entry *r = get_packed_ref(refname);
+		if (r) {
+			if (peel_entry(r, 0))
+				return -1;
 			hashcpy(sha1, r->u.value.peeled);
 			return 0;
 		}
 	}
 
-fallback:
-	o = lookup_unknown_object(base);
-	if (o->type == OBJ_NONE) {
-		int type = sha1_object_info(base, NULL);
-		if (type < 0)
-			return -1;
-		o->type = type;
-	}
-
-	if (o->type == OBJ_TAG) {
-		o = deref_tag_noverify(o);
-		if (o) {
-			hashcpy(sha1, o->sha1);
-			return 0;
-		}
-	}
-	return -1;
+	return peel_object(base, sha1);
 }
 
 struct warn_if_dangling_data {
@@ -1316,10 +1506,16 @@ void warn_dangling_symref(FILE *fp, const char *msg_fmt, const char *refname)
 	for_each_rawref(warn_if_dangling_symref, &data);
 }
 
-static int do_for_each_ref(const char *submodule, const char *base, each_ref_fn fn,
-			   int trim, int flags, void *cb_data)
+/*
+ * Call fn for each reference in the specified ref_cache, omitting
+ * references not in the containing_dir of base.  fn is called for all
+ * references, including broken ones.  If fn ever returns a non-zero
+ * value, stop the iteration and return that value; otherwise, return
+ * 0.
+ */
+static int do_for_each_entry(struct ref_cache *refs, const char *base,
+			     each_ref_entry_fn fn, void *cb_data)
 {
-	struct ref_cache *refs = get_ref_cache(submodule);
 	struct ref_dir *packed_dir = get_packed_refs(refs);
 	struct ref_dir *loose_dir = get_loose_refs(refs);
 	int retval = 0;
@@ -1332,24 +1528,43 @@ static int do_for_each_ref(const char *submodule, const char *base, each_ref_fn
 	if (packed_dir && loose_dir) {
 		sort_ref_dir(packed_dir);
 		sort_ref_dir(loose_dir);
-		retval = do_for_each_ref_in_dirs(
-				packed_dir, loose_dir,
-				base, fn, trim, flags, cb_data);
+		retval = do_for_each_entry_in_dirs(
+				packed_dir, loose_dir, fn, cb_data);
 	} else if (packed_dir) {
 		sort_ref_dir(packed_dir);
-		retval = do_for_each_ref_in_dir(
-				packed_dir, 0,
-				base, fn, trim, flags, cb_data);
+		retval = do_for_each_entry_in_dir(
+				packed_dir, 0, fn, cb_data);
 	} else if (loose_dir) {
 		sort_ref_dir(loose_dir);
-		retval = do_for_each_ref_in_dir(
-				loose_dir, 0,
-				base, fn, trim, flags, cb_data);
+		retval = do_for_each_entry_in_dir(
+				loose_dir, 0, fn, cb_data);
 	}
 
 	return retval;
 }
 
+/*
+ * Call fn for each reference in the specified ref_cache for which the
+ * refname begins with base.  If trim is non-zero, then trim that many
+ * characters off the beginning of each refname before passing the
+ * refname to fn.  flags can be DO_FOR_EACH_INCLUDE_BROKEN to include
+ * broken references in the iteration.  If fn ever returns a non-zero
+ * value, stop the iteration and return that value; otherwise, return
+ * 0.
+ */
+static int do_for_each_ref(struct ref_cache *refs, const char *base,
+			   each_ref_fn fn, int trim, int flags, void *cb_data)
+{
+	struct ref_entry_cb data;
+	data.base = base;
+	data.trim = trim;
+	data.flags = flags;
+	data.fn = fn;
+	data.cb_data = cb_data;
+
+	return do_for_each_entry(refs, base, do_one_ref, &data);
+}
+
 static int do_head_ref(const char *submodule, each_ref_fn fn, void *cb_data)
 {
 	unsigned char sha1[20];
@@ -1380,23 +1595,23 @@ int head_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
 
 int for_each_ref(each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(NULL, "", fn, 0, 0, cb_data);
+	return do_for_each_ref(&ref_cache, "", fn, 0, 0, cb_data);
 }
 
 int for_each_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(submodule, "", fn, 0, 0, cb_data);
+	return do_for_each_ref(get_ref_cache(submodule), "", fn, 0, 0, cb_data);
 }
 
 int for_each_ref_in(const char *prefix, each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(NULL, prefix, fn, strlen(prefix), 0, cb_data);
+	return do_for_each_ref(&ref_cache, prefix, fn, strlen(prefix), 0, cb_data);
 }
 
 int for_each_ref_in_submodule(const char *submodule, const char *prefix,
 		each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(submodule, prefix, fn, strlen(prefix), 0, cb_data);
+	return do_for_each_ref(get_ref_cache(submodule), prefix, fn, strlen(prefix), 0, cb_data);
 }
 
 int for_each_tag_ref(each_ref_fn fn, void *cb_data)
@@ -1431,7 +1646,7 @@ int for_each_remote_ref_submodule(const char *submodule, each_ref_fn fn, void *c
 
 int for_each_replace_ref(each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(NULL, "refs/replace/", fn, 13, 0, cb_data);
+	return do_for_each_ref(&ref_cache, "refs/replace/", fn, 13, 0, cb_data);
 }
 
 int head_ref_namespaced(each_ref_fn fn, void *cb_data)
@@ -1454,7 +1669,7 @@ int for_each_namespaced_ref(each_ref_fn fn, void *cb_data)
 	struct strbuf buf = STRBUF_INIT;
 	int ret;
 	strbuf_addf(&buf, "%srefs/", get_git_namespace());
-	ret = do_for_each_ref(NULL, buf.buf, fn, 0, 0, cb_data);
+	ret = do_for_each_ref(&ref_cache, buf.buf, fn, 0, 0, cb_data);
 	strbuf_release(&buf);
 	return ret;
 }
@@ -1496,7 +1711,7 @@ int for_each_glob_ref(each_ref_fn fn, const char *pattern, void *cb_data)
 
 int for_each_rawref(each_ref_fn fn, void *cb_data)
 {
-	return do_for_each_ref(NULL, "", fn, 0,
+	return do_for_each_ref(&ref_cache, "", fn, 0,
 			       DO_FOR_EACH_INCLUDE_BROKEN, cb_data);
 }
 
@@ -1702,7 +1917,7 @@ static struct ref_lock *lock_ref_sha1_basic(const char *refname,
 	 * name is a proper prefix of our refname.
 	 */
 	if (missing &&
-	     !is_refname_available(refname, NULL, get_packed_refs(get_ref_cache(NULL)))) {
+	     !is_refname_available(refname, NULL, get_packed_refs(&ref_cache))) {
 		last_errno = ENOTDIR;
 		goto error_return;
 	}
@@ -1754,47 +1969,224 @@ struct ref_lock *lock_any_ref_for_update(const char *refname,
 	return lock_ref_sha1_basic(refname, old_sha1, flags, NULL);
 }
 
-struct repack_without_ref_sb {
-	const char *refname;
-	int fd;
-};
-
-static int repack_without_ref_fn(const char *refname, const unsigned char *sha1,
-				 int flags, void *cb_data)
+/*
+ * Write an entry to the packed-refs file for the specified refname.
+ * If peeled is non-NULL, write it as the entry's peeled value.
+ */
+static void write_packed_entry(int fd, char *refname, unsigned char *sha1,
+			       unsigned char *peeled)
 {
-	struct repack_without_ref_sb *data = cb_data;
 	char line[PATH_MAX + 100];
 	int len;
 
-	if (!strcmp(data->refname, refname))
-		return 0;
 	len = snprintf(line, sizeof(line), "%s %s\n",
 		       sha1_to_hex(sha1), refname);
 	/* this should not happen but just being defensive */
 	if (len > sizeof(line))
 		die("too long a refname '%s'", refname);
-	write_or_die(data->fd, line, len);
+	write_or_die(fd, line, len);
+
+	if (peeled) {
+		if (snprintf(line, sizeof(line), "^%s\n",
+			     sha1_to_hex(peeled)) != PEELED_LINE_LENGTH)
+			die("internal error");
+		write_or_die(fd, line, PEELED_LINE_LENGTH);
+	}
+}
+
+struct ref_to_prune {
+	struct ref_to_prune *next;
+	unsigned char sha1[20];
+	char name[FLEX_ARRAY];
+};
+
+struct pack_refs_cb_data {
+	unsigned int flags;
+	struct ref_to_prune *ref_to_prune;
+	int fd;
+};
+
+static int pack_one_ref(struct ref_entry *entry, void *cb_data)
+{
+	struct pack_refs_cb_data *cb = cb_data;
+	enum peel_status peel_status;
+	int is_tag_ref = !prefixcmp(entry->name, "refs/tags/");
+
+	/* ALWAYS pack refs that were already packed or are tags */
+	if (!(cb->flags & PACK_REFS_ALL) && !is_tag_ref &&
+	    !(entry->flag & REF_ISPACKED))
+		return 0;
+
+	/* Do not pack symbolic or broken refs: */
+	if ((entry->flag & REF_ISSYMREF) || !ref_resolves_to_object(entry))
+		return 0;
+
+	peel_status = peel_entry(entry, 1);
+	if (peel_status != PEEL_PEELED && peel_status != PEEL_NON_TAG)
+		die("internal error peeling reference %s (%s)",
+		    entry->name, sha1_to_hex(entry->u.value.sha1));
+	write_packed_entry(cb->fd, entry->name, entry->u.value.sha1,
+			   peel_status == PEEL_PEELED ?
+			   entry->u.value.peeled : NULL);
+
+	/* If the ref was already packed, there is no need to prune it. */
+	if ((cb->flags & PACK_REFS_PRUNE) && !(entry->flag & REF_ISPACKED)) {
+		int namelen = strlen(entry->name) + 1;
+		struct ref_to_prune *n = xcalloc(1, sizeof(*n) + namelen);
+		hashcpy(n->sha1, entry->u.value.sha1);
+		strcpy(n->name, entry->name);
+		n->next = cb->ref_to_prune;
+		cb->ref_to_prune = n;
+	}
 	return 0;
 }
 
+/*
+ * Remove empty parents, but spare refs/ and immediate subdirs.
+ * Note: munges *name.
+ */
+static void try_remove_empty_parents(char *name)
+{
+	char *p, *q;
+	int i;
+	p = name;
+	for (i = 0; i < 2; i++) { /* refs/{heads,tags,...}/ */
+		while (*p && *p != '/')
+			p++;
+		/* tolerate duplicate slashes; see check_refname_format() */
+		while (*p == '/')
+			p++;
+	}
+	for (q = p; *q; q++)
+		;
+	while (1) {
+		while (q > p && *q != '/')
+			q--;
+		while (q > p && *(q-1) == '/')
+			q--;
+		if (q == p)
+			break;
+		*q = '\0';
+		if (rmdir(git_path("%s", name)))
+			break;
+	}
+}
+
+/* make sure nobody touched the ref, and unlink */
+static void prune_ref(struct ref_to_prune *r)
+{
+	struct ref_lock *lock = lock_ref_sha1(r->name + 5, r->sha1);
+
+	if (lock) {
+		unlink_or_warn(git_path("%s", r->name));
+		unlock_ref(lock);
+		try_remove_empty_parents(r->name);
+	}
+}
+
+static void prune_refs(struct ref_to_prune *r)
+{
+	while (r) {
+		prune_ref(r);
+		r = r->next;
+	}
+}
+
 static struct lock_file packlock;
 
-static int repack_without_ref(const char *refname)
+int pack_refs(unsigned int flags)
 {
-	struct repack_without_ref_sb data;
-	struct ref_cache *refs = get_ref_cache(NULL);
-	struct ref_dir *packed = get_packed_refs(refs);
-	if (find_ref(packed, refname) == NULL)
+	struct pack_refs_cb_data cbdata;
+
+	memset(&cbdata, 0, sizeof(cbdata));
+	cbdata.flags = flags;
+
+	cbdata.fd = hold_lock_file_for_update(&packlock, git_path("packed-refs"),
+					      LOCK_DIE_ON_ERROR);
+
+	write_or_die(cbdata.fd, PACKED_REFS_HEADER, strlen(PACKED_REFS_HEADER));
+
+	do_for_each_entry(&ref_cache, "", pack_one_ref, &cbdata);
+	if (commit_lock_file(&packlock) < 0)
+		die_errno("unable to overwrite old ref-pack file");
+	prune_refs(cbdata.ref_to_prune);
+	return 0;
+}
+
+static int repack_ref_fn(struct ref_entry *entry, void *cb_data)
+{
+	int *fd = cb_data;
+	enum peel_status peel_status;
+
+	if (entry->flag & REF_ISBROKEN) {
+		/* This shouldn't happen to packed refs. */
+		error("%s is broken!", entry->name);
 		return 0;
-	data.refname = refname;
-	data.fd = hold_lock_file_for_update(&packlock, git_path("packed-refs"), 0);
-	if (data.fd < 0) {
+	}
+	if (!has_sha1_file(entry->u.value.sha1)) {
+		unsigned char sha1[20];
+		int flags;
+
+		if (read_ref_full(entry->name, sha1, 0, &flags))
+			/* We should at least have found the packed ref. */
+			die("Internal error");
+		if ((flags & REF_ISSYMREF) || !(flags & REF_ISPACKED))
+			/*
+			 * This packed reference is overridden by a
+			 * loose reference, so it is OK that its value
+			 * is no longer valid; for example, it might
+			 * refer to an object that has been garbage
+			 * collected.  For this purpose we don't even
+			 * care whether the loose reference itself is
+			 * invalid, broken, symbolic, etc.  Silently
+			 * omit the packed reference from the output.
+			 */
+			return 0;
+		/*
+		 * There is no overriding loose reference, so the fact
+		 * that this reference doesn't refer to a valid object
+		 * indicates some kind of repository corruption.
+		 * Report the problem, then omit the reference from
+		 * the output.
+		 */
+		error("%s does not point to a valid object!", entry->name);
+		return 0;
+	}
+
+	peel_status = peel_entry(entry, 0);
+	write_packed_entry(*fd, entry->name, entry->u.value.sha1,
+			   peel_status == PEEL_PEELED ?
+			   entry->u.value.peeled : NULL);
+
+	return 0;
+}
+
+static int repack_without_ref(const char *refname)
+{
+	int fd;
+	struct ref_dir *packed;
+
+	if (!get_packed_ref(refname))
+		return 0; /* refname does not exist in packed refs */
+
+	fd = hold_lock_file_for_update(&packlock, git_path("packed-refs"), 0);
+	if (fd < 0) {
 		unable_to_lock_error(git_path("packed-refs"), errno);
 		return error("cannot delete '%s' from packed refs", refname);
 	}
-	clear_packed_ref_cache(refs);
-	packed = get_packed_refs(refs);
-	do_for_each_ref_in_dir(packed, 0, "", repack_without_ref_fn, 0, 0, &data);
+	clear_packed_ref_cache(&ref_cache);
+	packed = get_packed_refs(&ref_cache);
+	/* Remove refname from the cache. */
+	if (remove_entry(packed, refname) == -1) {
+		/*
+		 * The packed entry disappeared while we were
+		 * acquiring the lock.
+		 */
+		rollback_lock_file(&packlock);
+		return 0;
+	}
+	write_or_die(fd, PACKED_REFS_HEADER, strlen(PACKED_REFS_HEADER));
+	do_for_each_entry_in_dir(packed, 0, repack_ref_fn, &fd);
 	return commit_lock_file(&packlock);
 }
 
@@ -1823,7 +2215,7 @@ int delete_ref(const char *refname, const unsigned char *sha1, int delopt)
 	ret |= repack_without_ref(lock->ref_name);
 
 	unlink_or_warn(git_path("logs/%s", lock->ref_name));
-	invalidate_ref_cache(NULL);
+	clear_loose_ref_cache(&ref_cache);
 	unlock_ref(lock);
 	return ret;
 }
@@ -1845,7 +2237,6 @@ int rename_ref(const char *oldrefname, const char *newrefname, const char *logms
 	struct stat loginfo;
 	int log = !lstat(git_path("logs/%s", oldrefname), &loginfo);
 	const char *symref = NULL;
-	struct ref_cache *refs = get_ref_cache(NULL);
 
 	if (log && S_ISLNK(loginfo.st_mode))
 		return error("reflog for %s is a symlink", oldrefname);
@@ -1857,10 +2248,10 @@ int rename_ref(const char *oldrefname, const char *newrefname, const char *logms
 	if (!symref)
 		return error("refname %s not found", oldrefname);
 
-	if (!is_refname_available(newrefname, oldrefname, get_packed_refs(refs)))
+	if (!is_refname_available(newrefname, oldrefname, get_packed_refs(&ref_cache)))
 		return 1;
 
-	if (!is_refname_available(newrefname, oldrefname, get_loose_refs(refs)))
+	if (!is_refname_available(newrefname, oldrefname, get_loose_refs(&ref_cache)))
 		return 1;
 
 	if (log && rename(git_path("logs/%s", oldrefname), git_path(TMP_RENAMED_LOG)))
@@ -2116,7 +2507,7 @@ int write_ref_sha1(struct ref_lock *lock,
 		unlock_ref(lock);
 		return -1;
 	}
-	clear_loose_ref_cache(get_ref_cache(NULL));
+	clear_loose_ref_cache(&ref_cache);
 	if (log_ref_write(lock->ref_name, lock->old_sha1, sha1, logmsg) < 0 ||
 	    (strcmp(lock->ref_name, lock->orig_ref_name) &&
 	     log_ref_write(lock->orig_ref_name, lock->old_sha1, sha1, logmsg) < 0)) {
diff --git a/refs.h b/refs.h
index a35eafc4ee..8060ed8313 100644
--- a/refs.h
+++ b/refs.h
@@ -10,8 +10,21 @@ struct ref_lock {
 	int force_write;
 };
 
+/*
+ * Bit values set in the flags argument passed to each_ref_fn():
+ */
+
+/* Reference is a symbolic reference. */
 #define REF_ISSYMREF 0x01
+
+/* Reference is a packed reference. */
 #define REF_ISPACKED 0x02
+
+/*
+ * Reference cannot be resolved to an object name: dangling symbolic
+ * reference (directly or indirectly), corrupt reference file, or
+ * symbolic reference refers to ill-formatted reference name.
+ */
 #define REF_ISBROKEN 0x04
 
 /*
@@ -59,8 +72,30 @@ extern void warn_dangling_symref(FILE *fp, const char *msg_fmt, const char *refn
  */
 extern void add_packed_ref(const char *refname, const unsigned char *sha1);
 
+/*
+ * Flags for controlling behaviour of pack_refs()
+ * PACK_REFS_PRUNE: Prune loose refs after packing
+ * PACK_REFS_ALL:   Pack _all_ refs, not just tags and already packed refs
+ */
+#define PACK_REFS_PRUNE 0x0001
+#define PACK_REFS_ALL   0x0002
+
+/*
+ * Write a packed-refs file for the current repository.
+ * flags: Combination of the above PACK_REFS_* flags.
+ */
+int pack_refs(unsigned int flags);
+
 extern int ref_exists(const char *);
 
+/*
+ * If refname is a non-symbolic reference that refers to a tag object,
+ * and the tag can be (recursively) dereferenced to a non-tag object,
+ * store the SHA1 of the referred-to object to sha1 and return 0.  If
+ * any of these conditions are not met, return a non-zero value.
+ * Symbolic references are considered unpeelable, even if they
+ * ultimately resolve to a peelable tag.
+ */
 extern int peel_ref(const char *refname, unsigned char *sha1);
 
 /** Locks a "refs/" ref returning the lock on success and NULL on failure. **/
diff --git a/t/t3210-pack-refs.sh b/t/t3210-pack-refs.sh
index cd04361df8..1a2080e3dc 100755
--- a/t/t3210-pack-refs.sh
+++ b/t/t3210-pack-refs.sh
@@ -118,4 +118,37 @@ test_expect_success 'pack, prune and repack' '
 	test_cmp all-of-them again
 '
 
+test_expect_success 'explicit pack-refs with dangling packed reference' '
+	git commit --allow-empty -m "soon to be garbage-collected" &&
+	git pack-refs --all &&
+	git reset --hard HEAD^ &&
+	git reflog expire --expire=all --all &&
+	git prune --expire=all &&
+	git pack-refs --all 2>result &&
+	test_cmp /dev/null result
+'
+
+test_expect_success 'delete ref with dangling packed version' '
+	git checkout -b lamb &&
+	git commit --allow-empty -m "future garbage" &&
+	git pack-refs --all &&
+	git reset --hard HEAD^ &&
+	git checkout master &&
+	git reflog expire --expire=all --all &&
+	git prune --expire=all &&
+	git branch -d lamb 2>result &&
+	test_cmp /dev/null result
+'
+
+test_expect_success 'delete ref while another dangling packed ref' '
+	git branch lamb &&
+	git commit --allow-empty -m "future garbage" &&
+	git pack-refs --all &&
+	git reset --hard HEAD^ &&
+	git reflog expire --expire=all --all &&
+	git prune --expire=all &&
+	git branch -d lamb 2>result &&
+	test_cmp /dev/null result
+'
+
 test_done
diff --git a/t/t3211-peel-ref.sh b/t/t3211-peel-ref.sh
index d4d7792eae..3b7caca421 100755
--- a/t/t3211-peel-ref.sh
+++ b/t/t3211-peel-ref.sh
@@ -61,4 +61,13 @@ test_expect_success 'refs are peeled outside of refs/tags (old packed)' '
 	test_cmp expect actual
 '
 
+test_expect_success 'peeled refs survive deletion of packed ref' '
+	git pack-refs --all &&
+	cp .git/packed-refs fully-peeled &&
+	git branch yadda &&
+	git pack-refs --all &&
+	git branch -d yadda &&
+	test_cmp fully-peeled .git/packed-refs
+'
+
 test_done