Merge branch 'nd/prune-in-worktree'

"git gc" and friends when multiple worktrees are used off of a
single repository did not consider the index and per-worktree refs
of other worktrees as the root for reachability traversal, making
objects that are in use only in other worktrees to be subject to
garbage collection.

* nd/prune-in-worktree:
  refs.c: reindent get_submodule_ref_store()
  refs.c: remove fallback-to-main-store code get_submodule_ref_store()
  rev-list: expose and document --single-worktree
  revision.c: --reflog add HEAD reflog from all worktrees
  files-backend: make reflog iterator go through per-worktree reflog
  revision.c: --all adds HEAD from all worktrees
  refs: remove dead for_each_*_submodule()
  refs.c: move for_each_remote_ref_submodule() to submodule.c
  revision.c: use refs_for_each*() instead of for_each_*_submodule()
  refs: add refs_head_ref()
  refs: move submodule slash stripping code to get_submodule_ref_store
  refs.c: refactor get_submodule_ref_store(), share common free block
  revision.c: --indexed-objects add objects from all worktrees
  revision.c: refactor add_index_objects_to_pending()
  refs.c: use is_dir_sep() in resolve_gitlink_ref()
  revision.h: new flag in struct rev_info wrt. worktree-related refs

13 files changed, 308 insertions, 136 deletions

diff --git a/Documentation/rev-list-options.txt b/Documentation/rev-list-options.txt
index a6cf9eb38..7d860bfca 100644
--- a/Documentation/rev-list-options.txt
+++ b/Documentation/rev-list-options.txt
@@ -184,6 +184,14 @@ explicitly.
 	Pretend as if all objects mentioned by reflogs are listed on the
 	command line as `<commit>`.
 
+--single-worktree::
+	By default, all working trees will be examined by the
+	following options when there are more than one (see
+	linkgit:git-worktree[1]): `--all`, `--reflog` and
+	`--indexed-objects`.
+	This option forces them to examine the current working tree
+	only.
+
 --ignore-missing::
 	Upon seeing an invalid object name in the input, pretend as if
 	the bad input was not given.
diff --git a/Documentation/technical/api-ref-iteration.txt b/Documentation/technical/api-ref-iteration.txt
index 37379d833..46c3d5c35 100644
--- a/Documentation/technical/api-ref-iteration.txt
+++ b/Documentation/technical/api-ref-iteration.txt
@@ -32,11 +32,8 @@ Iteration functions
 
 * `for_each_glob_ref_in()` the previous and `for_each_ref_in()` combined.
 
-* `head_ref_submodule()`, `for_each_ref_submodule()`,
-  `for_each_ref_in_submodule()`, `for_each_tag_ref_submodule()`,
-  `for_each_branch_ref_submodule()`, `for_each_remote_ref_submodule()`
-  do the same as the functions described above but for a specified
-  submodule.
+* Use `refs_` API for accessing submodules. The submodule ref store could
+  be obtained with `get_submodule_ref_store()`.
 
 * `for_each_rawref()` can be used to learn about broken ref and symref.
 
diff --git a/reachable.c b/reachable.c
index d1ac5d97e..88d7d679d 100644
--- a/reachable.c
+++ b/reachable.c
@@ -10,6 +10,7 @@
 #include "progress.h"
 #include "list-objects.h"
 #include "packfile.h"
+#include "worktree.h"
 
 struct connectivity_progress {
 	struct progress *progress;
@@ -177,6 +178,7 @@ void mark_reachable_objects(struct rev_info *revs, int mark_reflog,
 
 	/* detached HEAD is not included in the list above */
 	head_ref(add_one_ref, revs);
+	other_head_refs(add_one_ref, revs);
 
 	/* Add all reflog info */
 	if (mark_reflog)
diff --git a/refs.c b/refs.c
index b0106b816..a2b97fba7 100644
--- a/refs.c
+++ b/refs.c
@@ -336,12 +336,6 @@ int for_each_tag_ref(each_ref_fn fn, void *cb_data)
 	return refs_for_each_tag_ref(get_main_ref_store(), fn, cb_data);
 }
 
-int for_each_tag_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
-{
-	return refs_for_each_tag_ref(get_submodule_ref_store(submodule),
-				     fn, cb_data);
-}
-
 int refs_for_each_branch_ref(struct ref_store *refs, each_ref_fn fn, void *cb_data)
 {
 	return refs_for_each_ref_in(refs, "refs/heads/", fn, cb_data);
@@ -352,12 +346,6 @@ int for_each_branch_ref(each_ref_fn fn, void *cb_data)
 	return refs_for_each_branch_ref(get_main_ref_store(), fn, cb_data);
 }
 
-int for_each_branch_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
-{
-	return refs_for_each_branch_ref(get_submodule_ref_store(submodule),
-					fn, cb_data);
-}
-
 int refs_for_each_remote_ref(struct ref_store *refs, each_ref_fn fn, void *cb_data)
 {
 	return refs_for_each_ref_in(refs, "refs/remotes/", fn, cb_data);
@@ -368,12 +356,6 @@ int for_each_remote_ref(each_ref_fn fn, void *cb_data)
 	return refs_for_each_remote_ref(get_main_ref_store(), fn, cb_data);
 }
 
-int for_each_remote_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
-{
-	return refs_for_each_remote_ref(get_submodule_ref_store(submodule),
-					fn, cb_data);
-}
-
 int head_ref_namespaced(each_ref_fn fn, void *cb_data)
 {
 	struct strbuf buf = STRBUF_INIT;
@@ -1266,19 +1248,13 @@ int refs_rename_ref_available(struct ref_store *refs,
 	return ok;
 }
 
-int head_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
+int refs_head_ref(struct ref_store *refs, each_ref_fn fn, void *cb_data)
 {
 	struct object_id oid;
 	int flag;
 
-	if (submodule) {
-		if (resolve_gitlink_ref(submodule, "HEAD", oid.hash) == 0)
-			return fn("HEAD", &oid, 0, cb_data);
-
-		return 0;
-	}
-
-	if (!read_ref_full("HEAD", RESOLVE_REF_READING, oid.hash, &flag))
+	if (!refs_read_ref_full(refs, "HEAD", RESOLVE_REF_READING,
+				oid.hash, &flag))
 		return fn("HEAD", &oid, flag, cb_data);
 
 	return 0;
@@ -1286,7 +1262,7 @@ int head_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
 
 int head_ref(each_ref_fn fn, void *cb_data)
 {
-	return head_ref_submodule(NULL, fn, cb_data);
+	return refs_head_ref(get_main_ref_store(), fn, cb_data);
 }
 
 struct ref_iterator *refs_ref_iterator_begin(
@@ -1344,11 +1320,6 @@ int for_each_ref(each_ref_fn fn, void *cb_data)
 	return refs_for_each_ref(get_main_ref_store(), fn, cb_data);
 }
 
-int for_each_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data)
-{
-	return refs_for_each_ref(get_submodule_ref_store(submodule), fn, cb_data);
-}
-
 int refs_for_each_ref_in(struct ref_store *refs, const char *prefix,
 			 each_ref_fn fn, void *cb_data)
 {
@@ -1370,23 +1341,15 @@ int for_each_fullref_in(const char *prefix, each_ref_fn fn, void *cb_data, unsig
 			       prefix, fn, 0, flag, cb_data);
 }
 
-int for_each_ref_in_submodule(const char *submodule, const char *prefix,
-			      each_ref_fn fn, void *cb_data)
-{
-	return refs_for_each_ref_in(get_submodule_ref_store(submodule),
-				    prefix, fn, cb_data);
-}
-
-int for_each_fullref_in_submodule(const char *submodule, const char *prefix,
-				  each_ref_fn fn, void *cb_data,
-				  unsigned int broken)
+int refs_for_each_fullref_in(struct ref_store *refs, const char *prefix,
+			     each_ref_fn fn, void *cb_data,
+			     unsigned int broken)
 {
 	unsigned int flag = 0;
 
 	if (broken)
 		flag = DO_FOR_EACH_INCLUDE_BROKEN;
-	return do_for_each_ref(get_submodule_ref_store(submodule),
-			       prefix, fn, 0, flag, cb_data);
+	return do_for_each_ref(refs, prefix, fn, 0, flag, cb_data);
 }
 
 int for_each_replace_ref(each_ref_fn fn, void *cb_data)
@@ -1521,25 +1484,10 @@ const char *resolve_ref_unsafe(const char *refname, int resolve_flags,
 int resolve_gitlink_ref(const char *submodule, const char *refname,
 			unsigned char *sha1)
 {
-	size_t len = strlen(submodule);
 	struct ref_store *refs;
 	int flags;
 
-	while (len && submodule[len - 1] == '/')
-		len--;
-
-	if (!len)
-		return -1;
-
-	if (submodule[len]) {
-		/* We need to strip off one or more trailing slashes */
-		char *stripped = xmemdupz(submodule, len);
-
-		refs = get_submodule_ref_store(stripped);
-		free(stripped);
-	} else {
-		refs = get_submodule_ref_store(submodule);
-	}
+	refs = get_submodule_ref_store(submodule);
 
 	if (!refs)
 		return -1;
@@ -1654,31 +1602,32 @@ struct ref_store *get_submodule_ref_store(const char *submodule)
 {
 	struct strbuf submodule_sb = STRBUF_INIT;
 	struct ref_store *refs;
-	int ret;
+	char *to_free = NULL;
+	size_t len;
 
-	if (!submodule || !*submodule) {
-		/*
-		 * FIXME: This case is ideally not allowed. But that
-		 * can't happen until we clean up all the callers.
-		 */
-		return get_main_ref_store();
-	}
+	if (!submodule)
+		return NULL;
+
+	len = strlen(submodule);
+	while (len && is_dir_sep(submodule[len - 1]))
+		len--;
+	if (!len)
+		return NULL;
+
+	if (submodule[len])
+		/* We need to strip off one or more trailing slashes */
+		submodule = to_free = xmemdupz(submodule, len);
 
 	refs = lookup_ref_store_map(&submodule_ref_stores, submodule);
 	if (refs)
-		return refs;
+		goto done;
 
 	strbuf_addstr(&submodule_sb, submodule);
-	ret = is_nonbare_repository_dir(&submodule_sb);
-	strbuf_release(&submodule_sb);
-	if (!ret)
-		return NULL;
+	if (!is_nonbare_repository_dir(&submodule_sb))
+		goto done;
 
-	ret = submodule_to_gitdir(&submodule_sb, submodule);
-	if (ret) {
-		strbuf_release(&submodule_sb);
-		return NULL;
-	}
+	if (submodule_to_gitdir(&submodule_sb, submodule))
+		goto done;
 
 	/* assume that add_submodule_odb() has been called */
 	refs = ref_store_init(submodule_sb.buf,
@@ -1686,7 +1635,10 @@ struct ref_store *get_submodule_ref_store(const char *submodule)
 	register_ref_store_map(&submodule_ref_stores, "submodule",
 			       refs, submodule);
 
+done:
 	strbuf_release(&submodule_sb);
+	free(to_free);
+
 	return refs;
 }
 
diff --git a/refs.h b/refs.h
index 6daa78eb5..78a26400b 100644
--- a/refs.h
+++ b/refs.h
@@ -275,6 +275,8 @@ typedef int each_ref_fn(const char *refname,
  * modifies the reference also returns a nonzero value to immediately
  * stop the iteration. Returned references are sorted.
  */
+int refs_head_ref(struct ref_store *refs,
+		  each_ref_fn fn, void *cb_data);
 int refs_for_each_ref(struct ref_store *refs,
 		      each_ref_fn fn, void *cb_data);
 int refs_for_each_ref_in(struct ref_store *refs, const char *prefix,
@@ -289,6 +291,9 @@ int refs_for_each_remote_ref(struct ref_store *refs,
 int head_ref(each_ref_fn fn, void *cb_data);
 int for_each_ref(each_ref_fn fn, void *cb_data);
 int for_each_ref_in(const char *prefix, each_ref_fn fn, void *cb_data);
+int refs_for_each_fullref_in(struct ref_store *refs, const char *prefix,
+			     each_ref_fn fn, void *cb_data,
+			     unsigned int broken);
 int for_each_fullref_in(const char *prefix, each_ref_fn fn, void *cb_data,
 			unsigned int broken);
 int for_each_tag_ref(each_ref_fn fn, void *cb_data);
@@ -299,21 +304,6 @@ int for_each_glob_ref(each_ref_fn fn, const char *pattern, void *cb_data);
 int for_each_glob_ref_in(each_ref_fn fn, const char *pattern,
 			 const char *prefix, void *cb_data);
 
-int head_ref_submodule(const char *submodule, each_ref_fn fn, void *cb_data);
-int for_each_ref_submodule(const char *submodule,
-			   each_ref_fn fn, void *cb_data);
-int for_each_ref_in_submodule(const char *submodule, const char *prefix,
-			      each_ref_fn fn, void *cb_data);
-int for_each_fullref_in_submodule(const char *submodule, const char *prefix,
-				  each_ref_fn fn, void *cb_data,
-				  unsigned int broken);
-int for_each_tag_ref_submodule(const char *submodule,
-			       each_ref_fn fn, void *cb_data);
-int for_each_branch_ref_submodule(const char *submodule,
-				  each_ref_fn fn, void *cb_data);
-int for_each_remote_ref_submodule(const char *submodule,
-				  each_ref_fn fn, void *cb_data);
-
 int head_ref_namespaced(each_ref_fn fn, void *cb_data);
 int for_each_namespaced_ref(each_ref_fn fn, void *cb_data);
 
diff --git a/refs/files-backend.c b/refs/files-backend.c
index 3a7bf6a14..cda790dcb 100644
--- a/refs/files-backend.c
+++ b/refs/files-backend.c
@@ -106,15 +106,6 @@ static void files_reflog_path(struct files_ref_store *refs,
 			      struct strbuf *sb,
 			      const char *refname)
 {
-	if (!refname) {
-		/*
-		 * FIXME: of course this is wrong in multi worktree
-		 * setting. To be fixed real soon.
-		 */
-		strbuf_addf(sb, "%s/logs", refs->gitcommondir);
-		return;
-	}
-
 	switch (ref_type(refname)) {
 	case REF_TYPE_PER_WORKTREE:
 	case REF_TYPE_PSEUDOREF:
@@ -2059,23 +2050,63 @@ static struct ref_iterator_vtable files_reflog_iterator_vtable = {
 	files_reflog_iterator_abort
 };
 
-static struct ref_iterator *files_reflog_iterator_begin(struct ref_store *ref_store)
+static struct ref_iterator *reflog_iterator_begin(struct ref_store *ref_store,
+						  const char *gitdir)
 {
-	struct files_ref_store *refs =
-		files_downcast(ref_store, REF_STORE_READ,
-			       "reflog_iterator_begin");
 	struct files_reflog_iterator *iter = xcalloc(1, sizeof(*iter));
 	struct ref_iterator *ref_iterator = &iter->base;
 	struct strbuf sb = STRBUF_INIT;
 
 	base_ref_iterator_init(ref_iterator, &files_reflog_iterator_vtable);
-	files_reflog_path(refs, &sb, NULL);
+	strbuf_addf(&sb, "%s/logs", gitdir);
 	iter->dir_iterator = dir_iterator_begin(sb.buf);
 	iter->ref_store = ref_store;
 	strbuf_release(&sb);
+
 	return ref_iterator;
 }
 
+static enum iterator_selection reflog_iterator_select(
+	struct ref_iterator *iter_worktree,
+	struct ref_iterator *iter_common,
+	void *cb_data)
+{
+	if (iter_worktree) {
+		/*
+		 * We're a bit loose here. We probably should ignore
+		 * common refs if they are accidentally added as
+		 * per-worktree refs.
+		 */
+		return ITER_SELECT_0;
+	} else if (iter_common) {
+		if (ref_type(iter_common->refname) == REF_TYPE_NORMAL)
+			return ITER_SELECT_1;
+
+		/*
+		 * The main ref store may contain main worktree's
+		 * per-worktree refs, which should be ignored
+		 */
+		return ITER_SKIP_1;
+	} else
+		return ITER_DONE;
+}
+
+static struct ref_iterator *files_reflog_iterator_begin(struct ref_store *ref_store)
+{
+	struct files_ref_store *refs =
+		files_downcast(ref_store, REF_STORE_READ,
+			       "reflog_iterator_begin");
+
+	if (!strcmp(refs->gitdir, refs->gitcommondir)) {
+		return reflog_iterator_begin(ref_store, refs->gitcommondir);
+	} else {
+		return merge_ref_iterator_begin(
+			reflog_iterator_begin(ref_store, refs->gitdir),
+			reflog_iterator_begin(ref_store, refs->gitcommondir),
+			reflog_iterator_select, refs);
+	}
+}
+
 /*
  * If update is a direct update of head_ref (the reference pointed to
  * by HEAD), then add an extra REF_LOG_ONLY update for HEAD.
diff --git a/revision.c b/revision.c
index 94a5e9852..f9a90d71d 100644
--- a/revision.c
+++ b/revision.c
@@ -20,6 +20,7 @@
 #include "cache-tree.h"
 #include "bisect.h"
 #include "packfile.h"
+#include "worktree.h"
 
 volatile show_early_output_fn_t show_early_output;
 
@@ -1132,6 +1133,7 @@ struct all_refs_cb {
 	int warned_bad_reflog;
 	struct rev_info *all_revs;
 	const char *name_for_errormsg;
+	struct ref_store *refs;
 };
 
 int ref_excluded(struct string_list *ref_excludes, const char *path)
@@ -1168,6 +1170,7 @@ static void init_all_refs_cb(struct all_refs_cb *cb, struct rev_info *revs,
 	cb->all_revs = revs;
 	cb->all_flags = flags;
 	revs->rev_input_given = 1;
+	cb->refs = NULL;
 }
 
 void clear_ref_exclusion(struct string_list **ref_excludes_p)
@@ -1188,12 +1191,19 @@ void add_ref_exclusion(struct string_list **ref_excludes_p, const char *exclude)
 	string_list_append(*ref_excludes_p, exclude);
 }
 
-static void handle_refs(const char *submodule, struct rev_info *revs, unsigned flags,
-		int (*for_each)(const char *, each_ref_fn, void *))
+static void handle_refs(struct ref_store *refs,
+			struct rev_info *revs, unsigned flags,
+			int (*for_each)(struct ref_store *, each_ref_fn, void *))
 {
 	struct all_refs_cb cb;
+
+	if (!refs) {
+		/* this could happen with uninitialized submodules */
+		return;
+	}
+
 	init_all_refs_cb(&cb, revs, flags);
-	for_each(submodule, handle_one_ref, &cb);
+	for_each(refs, handle_one_ref, &cb);
 }
 
 static void handle_one_reflog_commit(struct object_id *oid, void *cb_data)
@@ -1229,17 +1239,41 @@ static int handle_one_reflog(const char *path, const struct object_id *oid,
 	struct all_refs_cb *cb = cb_data;
 	cb->warned_bad_reflog = 0;
 	cb->name_for_errormsg = path;
-	for_each_reflog_ent(path, handle_one_reflog_ent, cb_data);
+	refs_for_each_reflog_ent(cb->refs, path,
+				 handle_one_reflog_ent, cb_data);
 	return 0;
 }
 
+static void add_other_reflogs_to_pending(struct all_refs_cb *cb)
+{
+	struct worktree **worktrees, **p;
+
+	worktrees = get_worktrees(0);
+	for (p = worktrees; *p; p++) {
+		struct worktree *wt = *p;
+
+		if (wt->is_current)
+			continue;
+
+		cb->refs = get_worktree_ref_store(wt);
+		refs_for_each_reflog(cb->refs,
+				     handle_one_reflog,
+				     cb);
+	}
+	free_worktrees(worktrees);
+}
+
 void add_reflogs_to_pending(struct rev_info *revs, unsigned flags)
 {
 	struct all_refs_cb cb;
 
 	cb.all_revs = revs;
 	cb.all_flags = flags;
+	cb.refs = get_main_ref_store();
 	for_each_reflog(handle_one_reflog, &cb);
+
+	if (!revs->single_worktree)
+		add_other_reflogs_to_pending(&cb);
 }
 
 static void add_cache_tree(struct cache_tree *it, struct rev_info *revs,
@@ -1263,13 +1297,13 @@ static void add_cache_tree(struct cache_tree *it, struct rev_info *revs,
 
 }
 
-void add_index_objects_to_pending(struct rev_info *revs, unsigned flags)
+static void do_add_index_objects_to_pending(struct rev_info *revs,
+					    struct index_state *istate)
 {
 	int i;
 
-	read_cache();
-	for (i = 0; i < active_nr; i++) {
-		struct cache_entry *ce = active_cache[i];
+	for (i = 0; i < istate->cache_nr; i++) {
+		struct cache_entry *ce = istate->cache[i];
 		struct blob *blob;
 
 		if (S_ISGITLINK(ce->ce_mode))
@@ -1282,13 +1316,39 @@ void add_index_objects_to_pending(struct rev_info *revs, unsigned flags)
 					     ce->ce_mode, ce->name);
 	}
 
-	if (active_cache_tree) {
+	if (istate->cache_tree) {
 		struct strbuf path = STRBUF_INIT;
-		add_cache_tree(active_cache_tree, revs, &path);
+		add_cache_tree(istate->cache_tree, revs, &path);
 		strbuf_release(&path);
 	}
 }
 
+void add_index_objects_to_pending(struct rev_info *revs, unsigned int flags)
+{
+	struct worktree **worktrees, **p;
+
+	read_cache();
+	do_add_index_objects_to_pending(revs, &the_index);
+
+	if (revs->single_worktree)
+		return;
+
+	worktrees = get_worktrees(0);
+	for (p = worktrees; *p; p++) {
+		struct worktree *wt = *p;
+		struct index_state istate = { NULL };
+
+		if (wt->is_current)
+			continue; /* current index already taken care of */
+
+		if (read_index_from(&istate,
+				    worktree_git_path(wt, "index")) > 0)
+			do_add_index_objects_to_pending(revs, &istate);
+		discard_index(&istate);
+	}
+	free_worktrees(worktrees);
+}
+
 static int add_parents_only(struct rev_info *revs, const char *arg_, int flags,
 			    int exclude_parent)
 {
@@ -2069,23 +2129,25 @@ void parse_revision_opt(struct rev_info *revs, struct parse_opt_ctx_t *ctx,
 	ctx->argc -= n;
 }
 
-static int for_each_bisect_ref(const char *submodule, each_ref_fn fn, void *cb_data, const char *term) {
+static int for_each_bisect_ref(struct ref_store *refs, each_ref_fn fn,
+			       void *cb_data, const char *term)
+{
 	struct strbuf bisect_refs = STRBUF_INIT;
 	int status;
 	strbuf_addf(&bisect_refs, "refs/bisect/%s", term);
-	status = for_each_fullref_in_submodule(submodule, bisect_refs.buf, fn, cb_data, 0);
+	status = refs_for_each_fullref_in(refs, bisect_refs.buf, fn, cb_data, 0);
 	strbuf_release(&bisect_refs);
 	return status;
 }
 
-static int for_each_bad_bisect_ref(const char *submodule, each_ref_fn fn, void *cb_data)
+static int for_each_bad_bisect_ref(struct ref_store *refs, each_ref_fn fn, void *cb_data)
 {
-	return for_each_bisect_ref(submodule, fn, cb_data, term_bad);
+	return for_each_bisect_ref(refs, fn, cb_data, term_bad);
 }
 
-static int for_each_good_bisect_ref(const char *submodule, each_ref_fn fn, void *cb_data)
+static int for_each_good_bisect_ref(struct ref_store *refs, each_ref_fn fn, void *cb_data)
 {
-	return for_each_bisect_ref(submodule, fn, cb_data, term_good);
+	return for_each_bisect_ref(refs, fn, cb_data, term_good);
 }
 
 static int handle_revision_pseudo_opt(const char *submodule,
@@ -2094,8 +2156,22 @@ static int handle_revision_pseudo_opt(const char *submodule,
 {
 	const char *arg = argv[0];
 	const char *optarg;
+	struct ref_store *refs;
 	int argcount;
 
+	if (submodule) {
+		/*
+		 * We need some something like get_submodule_worktrees()
+		 * before we can go through all worktrees of a submodule,
+		 * .e.g with adding all HEADs from --all, which is not
+		 * supported right now, so stick to single worktree.
+		 */
+		if (!revs->single_worktree)
+			die("BUG: --single-worktree cannot be used together with submodule");
+		refs = get_submodule_ref_store(submodule);
+	} else
+		refs = get_main_ref_store();
+
 	/*
 	 * NOTE!
 	 *
@@ -2107,22 +2183,29 @@ static int handle_revision_pseudo_opt(const char *submodule,
 	 * register it in the list at the top of handle_revision_opt.
 	 */
 	if (!strcmp(arg, "--all")) {
-		handle_refs(submodule, revs, *flags, for_each_ref_submodule);
-		handle_refs(submodule, revs, *flags, head_ref_submodule);
+		handle_refs(refs, revs, *flags, refs_for_each_ref);
+		handle_refs(refs, revs, *flags, refs_head_ref);
+		if (!revs->single_worktree) {
+			struct all_refs_cb cb;
+
+			init_all_refs_cb(&cb, revs, *flags);
+			other_head_refs(handle_one_ref, &cb);
+		}
 		clear_ref_exclusion(&revs->ref_excludes);
 	} else if (!strcmp(arg, "--branches")) {
-		handle_refs(submodule, revs, *flags, for_each_branch_ref_submodule);
+		handle_refs(refs, revs, *flags, refs_for_each_branch_ref);
 		clear_ref_exclusion(&revs->ref_excludes);
 	} else if (!strcmp(arg, "--bisect")) {
 		read_bisect_terms(&term_bad, &term_good);
-		handle_refs(submodule, revs, *flags, for_each_bad_bisect_ref);
-		handle_refs(submodule, revs, *flags ^ (UNINTERESTING | BOTTOM), for_each_good_bisect_ref);
+		handle_refs(refs, revs, *flags, for_each_bad_bisect_ref);
+		handle_refs(refs, revs, *flags ^ (UNINTERESTING | BOTTOM),
+			    for_each_good_bisect_ref);
 		revs->bisect = 1;
 	} else if (!strcmp(arg, "--tags")) {
-		handle_refs(submodule, revs, *flags, for_each_tag_ref_submodule);
+		handle_refs(refs, revs, *flags, refs_for_each_tag_ref);
 		clear_ref_exclusion(&revs->ref_excludes);
 	} else if (!strcmp(arg, "--remotes")) {
-		handle_refs(submodule, revs, *flags, for_each_remote_ref_submodule);
+		handle_refs(refs, revs, *flags, refs_for_each_remote_ref);
 		clear_ref_exclusion(&revs->ref_excludes);
 	} else if ((argcount = parse_long_opt("glob", argv, &optarg))) {
 		struct all_refs_cb cb;
@@ -2169,6 +2252,8 @@ static int handle_revision_pseudo_opt(const char *submodule,
 			return error("invalid argument to --no-walk");
 	} else if (!strcmp(arg, "--do-walk")) {
 		revs->no_walk = 0;
+	} else if (!strcmp(arg, "--single-worktree")) {
+		revs->single_worktree = 1;
 	} else {
 		return 0;
 	}
diff --git a/revision.h b/revision.h
index bc18487d6..3a3d3e2cf 100644
--- a/revision.h
+++ b/revision.h
@@ -96,6 +96,7 @@ struct rev_info {
 			topo_order:1,
 			simplify_merges:1,
 			simplify_by_decoration:1,
+			single_worktree:1,
 			tag_objects:1,
 			tree_objects:1,
 			blob_objects:1,
diff --git a/submodule.c b/submodule.c
index 3cea8221e..075c55f3c 100644
--- a/submodule.c
+++ b/submodule.c
@@ -69,6 +69,13 @@ int is_staging_gitmodules_ok(const struct index_state *istate)
 	return 1;
 }
 
+static int for_each_remote_ref_submodule(const char *submodule,
+					 each_ref_fn fn, void *cb_data)
+{
+	return refs_for_each_remote_ref(get_submodule_ref_store(submodule),
+					fn, cb_data);
+}
+
 /*
  * Try to update the "path" entry in the "submodule.<name>" section of the
  * .gitmodules file. Return 0 only if a .gitmodules file was found, a section
@@ -1627,6 +1634,8 @@ static int find_first_merges(struct object_array *result, const char *path,
 			oid_to_hex(&a->object.oid));
 	init_revisions(&revs, NULL);
 	rev_opts.submodule = path;
+	/* FIXME: can't handle linked worktrees in submodules yet */
+	revs.single_worktree = path != NULL;
 	setup_revisions(ARRAY_SIZE(rev_args)-1, rev_args, &revs, &rev_opts);
 
 	/* save all revisions from the above list that contain b */
diff --git a/t/t1407-worktree-ref-store.sh b/t/t1407-worktree-ref-store.sh
index 5df06f355..8842d0329 100755
--- a/t/t1407-worktree-ref-store.sh
+++ b/t/t1407-worktree-ref-store.sh
@@ -49,4 +49,34 @@ test_expect_success 'create_symref(FOO, refs/heads/master)' '
 	test_cmp expected actual
 '
 
+test_expect_success 'for_each_reflog()' '
+	echo $_z40 > .git/logs/PSEUDO-MAIN &&
+	mkdir -p     .git/logs/refs/bisect &&
+	echo $_z40 > .git/logs/refs/bisect/random &&
+
+	echo $_z40 > .git/worktrees/wt/logs/PSEUDO-WT &&
+	mkdir -p     .git/worktrees/wt/logs/refs/bisect &&
+	echo $_z40 > .git/worktrees/wt/logs/refs/bisect/wt-random &&
+
+	$RWT for-each-reflog | cut -c 42- | sort >actual &&
+	cat >expected <<-\EOF &&
+	HEAD 0x1
+	PSEUDO-WT 0x0
+	refs/bisect/wt-random 0x0
+	refs/heads/master 0x0
+	refs/heads/wt-master 0x0
+	EOF
+	test_cmp expected actual &&
+
+	$RMAIN for-each-reflog | cut -c 42- | sort >actual &&
+	cat >expected <<-\EOF &&
+	HEAD 0x1
+	PSEUDO-MAIN 0x0
+	refs/bisect/random 0x0
+	refs/heads/master 0x0
+	refs/heads/wt-master 0x0
+	EOF
+	test_cmp expected actual
+'
+
 test_done
diff --git a/t/t5304-prune.sh b/t/t5304-prune.sh
index 133b5842b..6694c19a1 100755
--- a/t/t5304-prune.sh
+++ b/t/t5304-prune.sh
@@ -283,4 +283,41 @@ test_expect_success 'prune: handle alternate object database' '
 	git -C B prune
 '
 
+test_expect_success 'prune: handle index in multiple worktrees' '
+	git worktree add second-worktree &&
+	echo "new blob for second-worktree" >second-worktree/blob &&
+	git -C second-worktree add blob &&
+	git prune --expire=now &&
+	git -C second-worktree show :blob >actual &&
+	test_cmp second-worktree/blob actual
+'
+
+test_expect_success 'prune: handle HEAD in multiple worktrees' '
+	git worktree add --detach third-worktree &&
+	echo "new blob for third-worktree" >third-worktree/blob &&
+	git -C third-worktree add blob &&
+	git -C third-worktree commit -m "third" &&
+	rm .git/worktrees/third-worktree/index &&
+	test_must_fail git -C third-worktree show :blob &&
+	git prune --expire=now &&
+	git -C third-worktree show HEAD:blob >actual &&
+	test_cmp third-worktree/blob actual
+'
+
+test_expect_success 'prune: handle HEAD reflog in multiple worktrees' '
+	git config core.logAllRefUpdates true &&
+	echo "lost blob for third-worktree" >expected &&
+	(
+		cd third-worktree &&
+		cat ../expected >blob &&
+		git add blob &&
+		git commit -m "second commit in third" &&
+		git reset --hard HEAD^
+	) &&
+	git prune --expire=now &&
+	SHA1=`git hash-object expected` &&
+	git -C third-worktree show "$SHA1" >actual &&
+	test_cmp expected actual
+'
+
 test_done
diff --git a/worktree.c b/worktree.c
index c0c5a2b37..8aaeea037 100644
--- a/worktree.c
+++ b/worktree.c
@@ -386,3 +386,25 @@ int submodule_uses_worktrees(const char *path)
 	closedir(dir);
 	return ret;
 }
+
+int other_head_refs(each_ref_fn fn, void *cb_data)
+{
+	struct worktree **worktrees, **p;
+	int ret = 0;
+
+	worktrees = get_worktrees(0);
+	for (p = worktrees; *p; p++) {
+		struct worktree *wt = *p;
+		struct ref_store *refs;
+
+		if (wt->is_current)
+			continue;
+
+		refs = get_worktree_ref_store(wt);
+		ret = refs_head_ref(refs, fn, cb_data);
+		if (ret)
+			break;
+	}
+	free_worktrees(worktrees);
+	return ret;
+}
diff --git a/worktree.h b/worktree.h
index 5ea5e503f..9276c81ae 100644
--- a/worktree.h
+++ b/worktree.h
@@ -1,6 +1,8 @@
 #ifndef WORKTREE_H
 #define WORKTREE_H
 
+#include "refs.h"
+
 struct worktree {
 	char *path;
 	char *id;
@@ -70,6 +72,12 @@ extern void free_worktrees(struct worktree **);
 extern const struct worktree *find_shared_symref(const char *symref,
 						 const char *target);
 
+/*
+ * Similar to head_ref() for all HEADs _except_ one from the current
+ * worktree, which is covered by head_ref().
+ */
+int other_head_refs(each_ref_fn fn, void *cb_data);
+
 int is_worktree_being_rebased(const struct worktree *wt, const char *target);
 int is_worktree_being_bisected(const struct worktree *wt, const char *target);