diff --git a/BRANCHES.md b/BRANCHES.md
new file mode 100644
index 00000000000000..cecee7cf7ba6ab
--- /dev/null
+++ b/BRANCHES.md
@@ -0,0 +1,53 @@
+Branches used in this repo
+==========================
+
+The document explains the branching structure that we are using in the VFSForGit repository as well as the forking strategy that we have adopted for contributing.
+
+Repo Branches
+-------------
+
+1. master
+
+    This will track the Git for Windows repository master branch
+
+2. vfs
+
+    Would like to use this branch as an ever-green branch that continually rebases the VFSForGit changes onto a windows ever-green branch that is on the core/master, so that we can detect when the patches for VFSForGit have issues or if we have a new version patches sent upstream git we can regenerate this branch.
+
+3. vs/master
+
+    This tracks with the Git for Windows repository vs/master branch and are the generated files for using a Visual Studio solution.
+
+4. vfs-#
+
+    These branches are used to track the specific version that match Git for Windows with the VFSForGit specific patches on top.  When a new version of Git for Windows is released, the VFSForGit patches will be rebased on that windows version and a new gvfs-# branch created to create pull requests against.
+
+    #### Examples
+
+    ```
+    vfs-2.20.0
+    vfs-2.20.1
+    ```
+
+    The versions of git for VFSForGit are based on the Git for Windows versions.  v2.20.0.vfs.1 will correspond with the v2.20.0.windows.1 with the VFSForGit specific patches applied to the windows version.
+
+Tags
+----
+
+We are using annotated tags to build the version number for git.  The build will look back through the commit history to find the first tag matching `v[0-9]*vfs*` and build the git version number using that tag.
+
+Forking
+-------
+
+A personal fork of this repository and a branch in that repository should be used for development.
+
+These branches should be based on the latest vfs-# branch.  If there are work in progress pull requests that you have based on a previous version branch when a new version branch is created, you will need to move your patches to the new branch to get them in that latest version.
+
+#### Example
+
+```
+git clone <personal fork repo URL>
+git remote add ms https://github.com/Microsoft/git.git
+git checkout -b my-changes ms/vfs-2.20.0 --no-track
+git push -fu origin HEAD
+```
diff --git a/Makefile b/Makefile
index 3f4bc82979d4a1..57891978afedf1 100644
--- a/Makefile
+++ b/Makefile
@@ -901,6 +901,7 @@ LIB_OBJS += gettext.o
 LIB_OBJS += gpg-interface.o
 LIB_OBJS += graph.o
 LIB_OBJS += grep.o
+LIB_OBJS += gvfs.o
 LIB_OBJS += hashmap.o
 LIB_OBJS += help.o
 LIB_OBJS += hex.o
diff --git a/apply.c b/apply.c
index 3f2c22bc96dbe0..d880cf877bbe11 100644
--- a/apply.c
+++ b/apply.c
@@ -3346,6 +3346,24 @@ static int checkout_target(struct index_state *istate,
 {
 	struct checkout costate = CHECKOUT_INIT;
 
+	/*
+	 * Do not checkout the entry if the skipworktree bit is set
+	 *
+	 * Both callers of this method (check_preimage and load_current)
+	 * check for the existance of the file before calling this
+	 * method so we know that the file doesn't exist at this point
+	 * and we don't need to perform that check again here.
+	 * We just need to check the skip-worktree and return.
+	 *
+	 * This is to prevent git from creating a file in the
+	 * working directory that has the skip-worktree bit on,
+	 * then updating the index from the patch and not keeping
+	 * the working directory version up to date with what it
+	 * changed the index version to be.
+	 */
+	if (ce_skip_worktree(ce))
+		return 0;
+
 	costate.refresh_cache = 1;
 	costate.istate = istate;
 	if (checkout_entry(ce, &costate, NULL, NULL) ||
diff --git a/builtin.h b/builtin.h
index 53fb290963377b..f8a86c8f8ab12f 100644
--- a/builtin.h
+++ b/builtin.h
@@ -226,6 +226,7 @@ int cmd_tag(int argc, const char **argv, const char *prefix);
 int cmd_tar_tree(int argc, const char **argv, const char *prefix);
 int cmd_unpack_file(int argc, const char **argv, const char *prefix);
 int cmd_unpack_objects(int argc, const char **argv, const char *prefix);
+int cmd_update(int argc, const char **argv, const char *prefix);
 int cmd_update_index(int argc, const char **argv, const char *prefix);
 int cmd_update_ref(int argc, const char **argv, const char *prefix);
 int cmd_update_server_info(int argc, const char **argv, const char *prefix);
diff --git a/builtin/gc.c b/builtin/gc.c
index 090959350e06c0..7c24ac46362c9e 100644
--- a/builtin/gc.c
+++ b/builtin/gc.c
@@ -12,6 +12,7 @@
 
 #include "builtin.h"
 #include "repository.h"
+#include "gvfs.h"
 #include "config.h"
 #include "tempfile.h"
 #include "lockfile.h"
@@ -586,6 +587,9 @@ int cmd_gc(int argc, const char **argv, const char *prefix)
 	if (quiet)
 		strvec_push(&repack, "-q");
 
+	if ((!auto_gc || (auto_gc && gc_auto_threshold > 0)) && gvfs_config_is_set(GVFS_BLOCK_COMMANDS))
+		die(_("'git gc' is not supported on a GVFS repo"));
+
 	if (auto_gc) {
 		/*
 		 * Auto-gc should be least intrusive as possible.
diff --git a/builtin/reset.c b/builtin/reset.c
index e56834e7cc0eed..7aa305439d4310 100644
--- a/builtin/reset.c
+++ b/builtin/reset.c
@@ -27,6 +27,7 @@
 #include "submodule-config.h"
 #include "strbuf.h"
 #include "quote.h"
+#include "dir.h"
 
 #define REFRESH_INDEX_DELAY_WARNING_IN_MS (2 * 1000)
 
@@ -130,12 +131,45 @@ static void update_index_from_diff(struct diff_queue_struct *q,
 		struct diff_options *opt, void *data)
 {
 	int i;
+	int pos;
 	int intent_to_add = *(int *)data;
 
 	for (i = 0; i < q->nr; i++) {
 		struct diff_filespec *one = q->queue[i]->one;
+		struct diff_filespec *two = q->queue[i]->two;
 		int is_missing = !(one->mode && !is_null_oid(&one->oid));
+		int was_missing = !two->mode && is_null_oid(&two->oid);
 		struct cache_entry *ce;
+		struct cache_entry *ceBefore;
+		struct checkout state = CHECKOUT_INIT;
+
+		/*
+		 * When using the sparse-checkout feature the cache entries that are
+		 * added here will not have the skip-worktree bit set.
+		 * Without this code there is data that is lost because the files that
+		 * would normally be in the working directory are not there and show as
+		 * deleted for the next status or in the case of added files just disappear.
+		 * We need to create the previous version of the files in the working
+		 * directory so that they will have the right content and the next
+		 * status call will show modified or untracked files correctly.
+		 */
+		if (core_apply_sparse_checkout && !file_exists(two->path))
+		{
+			pos = cache_name_pos(two->path, strlen(two->path));
+			if ((pos >= 0 && ce_skip_worktree(active_cache[pos])) && (is_missing || !was_missing))
+			{
+				state.force = 1;
+				state.refresh_cache = 1;
+				state.istate = &the_index;
+				ceBefore = make_cache_entry(&the_index, two->mode, &two->oid, two->path,
+					0, 0);
+				if (!ceBefore)
+					die(_("make_cache_entry failed for path '%s'"),
+						two->path);
+
+				checkout_entry(ceBefore, &state, NULL, NULL);
+			}
+		}
 
 		if (is_missing && !intent_to_add) {
 			remove_file_from_cache(one->path);
diff --git a/builtin/update-index.c b/builtin/update-index.c
index 79087bccea4b8b..669c5a411e6b73 100644
--- a/builtin/update-index.c
+++ b/builtin/update-index.c
@@ -18,6 +18,7 @@
 #include "dir.h"
 #include "split-index.h"
 #include "fsmonitor.h"
+#include "gvfs.h"
 
 /*
  * Default to not allowing changes to the list of files. The
@@ -1133,7 +1134,13 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 	argc = parse_options_end(&ctx);
 
 	getline_fn = nul_term_line ? strbuf_getline_nul : strbuf_getline_lf;
+	if (mark_skip_worktree_only && gvfs_config_is_set(GVFS_BLOCK_COMMANDS))
+		die(_("modifying the skip worktree bit is not supported on a GVFS repo"));
+	
 	if (preferred_index_format) {
+		if (preferred_index_format != 4 && gvfs_config_is_set(GVFS_BLOCK_COMMANDS))
+			die(_("changing the index version is not supported on a GVFS repo"));
+
 		if (preferred_index_format < INDEX_FORMAT_LB ||
 		    INDEX_FORMAT_UB < preferred_index_format)
 			die("index-version %d not in range: %d..%d",
@@ -1169,6 +1176,9 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 	}
 
 	if (split_index > 0) {
+		if (gvfs_config_is_set(GVFS_BLOCK_COMMANDS))
+			die(_("split index is not supported on a GVFS repo"));
+
 		if (git_config_get_split_index() == 0)
 			warning(_("core.splitIndex is set to false; "
 				  "remove or change it, if you really want to "
diff --git a/cache-tree.c b/cache-tree.c
index 9a59dafa26a07d..cc4dfd8c53d402 100644
--- a/cache-tree.c
+++ b/cache-tree.c
@@ -398,7 +398,29 @@ static int update_one(struct cache_tree *it,
 			continue;
 
 		strbuf_grow(&buffer, entlen + 100);
-		strbuf_addf(&buffer, "%o %.*s%c", mode, entlen, path + baselen, '\0');
+
+		switch (mode) {
+		case 0100644:
+			strbuf_add(&buffer, "100644 ", 7);
+			break;
+		case 0100664:
+			strbuf_add(&buffer, "100664 ", 7);
+			break;
+		case 0100755:
+			strbuf_add(&buffer, "100755 ", 7);
+			break;
+		case 0120000:
+			strbuf_add(&buffer, "120000 ", 7);
+			break;
+		case 0160000:
+			strbuf_add(&buffer, "160000 ", 7);
+			break;
+		default:
+			strbuf_addf(&buffer, "%o ", mode);
+			break;
+		}
+		strbuf_add(&buffer, path + baselen, entlen);
+		strbuf_addch(&buffer, '\0');
 		strbuf_add(&buffer, oid->hash, the_hash_algo->rawsz);
 
 #if DEBUG_CACHE_TREE
diff --git a/git.c b/git.c
index 4bdcdad2ccd3e7..5ccc764791a4e2 100644
--- a/git.c
+++ b/git.c
@@ -5,6 +5,8 @@
 #include "run-command.h"
 #include "alias.h"
 #include "shallow.h"
+#include "dir.h"
+#include "gvfs.h"
 
 #define RUN_SETUP		(1<<0)
 #define RUN_SETUP_GENTLY	(1<<1)
@@ -17,6 +19,7 @@
 #define SUPPORT_SUPER_PREFIX	(1<<4)
 #define DELAY_PAGER_CONFIG	(1<<5)
 #define NO_PARSEOPT		(1<<6) /* parse-options is not used */
+#define BLOCK_ON_GVFS_REPO	(1<<7) /* command not allowed in GVFS repos */
 
 struct cmd_struct {
 	const char *cmd;
@@ -405,6 +408,64 @@ static int handle_alias(int *argcp, const char ***argv)
 	return ret;
 }
 
+/* Runs pre/post-command hook */
+static struct strvec sargv = STRVEC_INIT;
+static int run_post_hook = 0;
+static int exit_code = -1;
+
+static int run_pre_command_hook(const char **argv)
+{
+	char *lock;
+	int ret = 0;
+
+	/*
+	 * Ensure the global pre/post command hook is only called for
+	 * the outer command and not when git is called recursively
+	 * or spawns multiple commands (like with the alias command)
+	 */
+	lock = getenv("COMMAND_HOOK_LOCK");
+	if (lock && !strcmp(lock, "true"))
+		return 0;
+	setenv("COMMAND_HOOK_LOCK", "true", 1);
+
+	/* call the hook proc */
+	strvec_pushv(&sargv, argv);
+	strvec_pushf(&sargv, "--git-pid=%"PRIuMAX, (uintmax_t)getpid());
+	ret = run_hook_strvec(NULL, "pre-command", &sargv);
+
+	if (!ret)
+		run_post_hook = 1;
+	return ret;
+}
+
+static int run_post_command_hook(void)
+{
+	char *lock;
+	int ret = 0;
+
+	/*
+	 * Only run post_command if pre_command succeeded in this process
+	 */
+	if (!run_post_hook)
+		return 0;
+	lock = getenv("COMMAND_HOOK_LOCK");
+	if (!lock || strcmp(lock, "true"))
+		return 0;
+
+	strvec_pushf(&sargv, "--exit_code=%u", exit_code);
+	ret = run_hook_strvec(NULL, "post-command", &sargv);
+
+	run_post_hook = 0;
+	strvec_clear(&sargv);
+	setenv("COMMAND_HOOK_LOCK", "false", 1);
+	return ret;
+}
+
+static void post_command_hook_atexit(void)
+{
+	run_post_command_hook();
+}
+
 static int run_builtin(struct cmd_struct *p, int argc, const char **argv)
 {
 	int status, help;
@@ -441,18 +502,26 @@ static int run_builtin(struct cmd_struct *p, int argc, const char **argv)
 	if (!help && p->option & NEED_WORK_TREE)
 		setup_work_tree();
 
+	if (!help && p->option & BLOCK_ON_GVFS_REPO && gvfs_config_is_set(GVFS_BLOCK_COMMANDS))
+		die("'git %s' is not supported on a GVFS repo", p->cmd);
+
+	if (run_pre_command_hook(argv))
+		die("pre-command hook aborted command");
+
 	trace_argv_printf(argv, "trace: built-in: git");
 	trace2_cmd_name(p->cmd);
 	trace2_cmd_list_config();
 	trace2_cmd_list_env_vars();
 
 	validate_cache_entries(the_repository->index);
-	status = p->fn(argc, argv, prefix);
+	exit_code = status = p->fn(argc, argv, prefix);
 	validate_cache_entries(the_repository->index);
 
 	if (status)
 		return status;
 
+	run_post_command_hook();
+
 	/* Somebody closed stdout? */
 	if (fstat(fileno(stdout), &st))
 		return 0;
@@ -517,7 +586,7 @@ static struct cmd_struct commands[] = {
 	{ "fmt-merge-msg", cmd_fmt_merge_msg, RUN_SETUP },
 	{ "for-each-ref", cmd_for_each_ref, RUN_SETUP },
 	{ "format-patch", cmd_format_patch, RUN_SETUP },
-	{ "fsck", cmd_fsck, RUN_SETUP },
+	{ "fsck", cmd_fsck, RUN_SETUP | BLOCK_ON_GVFS_REPO},
 	{ "fsck-objects", cmd_fsck, RUN_SETUP },
 	{ "gc", cmd_gc, RUN_SETUP },
 	{ "get-tar-commit-id", cmd_get_tar_commit_id, NO_PARSEOPT },
@@ -556,7 +625,7 @@ static struct cmd_struct commands[] = {
 	{ "pack-refs", cmd_pack_refs, RUN_SETUP },
 	{ "patch-id", cmd_patch_id, RUN_SETUP_GENTLY | NO_PARSEOPT },
 	{ "pickaxe", cmd_blame, RUN_SETUP },
-	{ "prune", cmd_prune, RUN_SETUP },
+	{ "prune", cmd_prune, RUN_SETUP | BLOCK_ON_GVFS_REPO},
 	{ "prune-packed", cmd_prune_packed, RUN_SETUP },
 	{ "pull", cmd_pull, RUN_SETUP | NEED_WORK_TREE },
 	{ "push", cmd_push, RUN_SETUP },
@@ -569,7 +638,7 @@ static struct cmd_struct commands[] = {
 	{ "remote", cmd_remote, RUN_SETUP },
 	{ "remote-ext", cmd_remote_ext, NO_PARSEOPT },
 	{ "remote-fd", cmd_remote_fd, NO_PARSEOPT },
-	{ "repack", cmd_repack, RUN_SETUP },
+	{ "repack", cmd_repack, RUN_SETUP | BLOCK_ON_GVFS_REPO },
 	{ "replace", cmd_replace, RUN_SETUP },
 	{ "rerere", cmd_rerere, RUN_SETUP },
 	{ "reset", cmd_reset, RUN_SETUP },
@@ -589,12 +658,14 @@ static struct cmd_struct commands[] = {
 	{ "stash", cmd_stash, RUN_SETUP | NEED_WORK_TREE },
 	{ "status", cmd_status, RUN_SETUP | NEED_WORK_TREE },
 	{ "stripspace", cmd_stripspace },
-	{ "submodule--helper", cmd_submodule__helper, RUN_SETUP | SUPPORT_SUPER_PREFIX | NO_PARSEOPT },
+	{ "submodule--helper", cmd_submodule__helper, RUN_SETUP | SUPPORT_SUPER_PREFIX | NO_PARSEOPT | BLOCK_ON_GVFS_REPO },
 	{ "switch", cmd_switch, RUN_SETUP | NEED_WORK_TREE },
 	{ "symbolic-ref", cmd_symbolic_ref, RUN_SETUP },
 	{ "tag", cmd_tag, RUN_SETUP | DELAY_PAGER_CONFIG },
 	{ "unpack-file", cmd_unpack_file, RUN_SETUP | NO_PARSEOPT },
 	{ "unpack-objects", cmd_unpack_objects, RUN_SETUP | NO_PARSEOPT },
+	{ "update", cmd_update },
+	{ "update-git-for-windows", cmd_update },
 	{ "update-index", cmd_update_index, RUN_SETUP },
 	{ "update-ref", cmd_update_ref, RUN_SETUP },
 	{ "update-server-info", cmd_update_server_info, RUN_SETUP },
@@ -607,7 +678,7 @@ static struct cmd_struct commands[] = {
 	{ "verify-tag", cmd_verify_tag, RUN_SETUP },
 	{ "version", cmd_version },
 	{ "whatchanged", cmd_whatchanged, RUN_SETUP },
-	{ "worktree", cmd_worktree, RUN_SETUP | NO_PARSEOPT },
+	{ "worktree", cmd_worktree, RUN_SETUP | NO_PARSEOPT | BLOCK_ON_GVFS_REPO },
 	{ "write-tree", cmd_write_tree, RUN_SETUP },
 };
 
@@ -728,13 +799,16 @@ static void execv_dashed_external(const char **argv)
 	 */
 	trace_argv_printf(cmd.args.v, "trace: exec:");
 
+	if (run_pre_command_hook(cmd.args.v))
+		die("pre-command hook aborted command");
+
 	/*
 	 * If we fail because the command is not found, it is
 	 * OK to return. Otherwise, we just pass along the status code,
 	 * or our usual generic code if we were not even able to exec
 	 * the program.
 	 */
-	status = run_command(&cmd);
+	exit_code = status = run_command(&cmd);
 
 	/*
 	 * If the child process ran and we are now going to exit, emit a
@@ -745,6 +819,8 @@ static void execv_dashed_external(const char **argv)
 		exit(status);
 	else if (errno != ENOENT)
 		exit(128);
+
+	run_post_command_hook();
 }
 
 static int run_argv(int *argcp, const char ***argv)
@@ -852,6 +928,7 @@ int cmd_main(int argc, const char **argv)
 	}
 
 	trace_command_performance(argv);
+	atexit(post_command_hook_atexit);
 
 	/*
 	 * "git-xxxx" is the same as "git xxxx", but we obviously:
@@ -879,10 +956,14 @@ int cmd_main(int argc, const char **argv)
 	} else {
 		/* The user didn't specify a command; give them help */
 		commit_pager_choice();
+		if (run_pre_command_hook(argv))
+			die("pre-command hook aborted command");
 		printf(_("usage: %s\n\n"), git_usage_string);
 		list_common_cmds_help();
 		printf("\n%s\n", _(git_more_info_string));
-		exit(1);
+		exit_code = 1;
+		run_post_command_hook();
+		exit(exit_code);
 	}
 	cmd = argv[0];
 
diff --git a/gvfs.c b/gvfs.c
new file mode 100644
index 00000000000000..4360d77075ea0f
--- /dev/null
+++ b/gvfs.c
@@ -0,0 +1,36 @@
+#include "cache.h"
+#include "gvfs.h"
+#include "config.h"
+
+static int gvfs_config_loaded;
+static int core_gvfs_is_bool;
+
+static int early_core_gvfs_config(const char *var, const char *value, void *data)
+{
+	if (!strcmp(var, "core.gvfs"))
+		core_gvfs = git_config_bool_or_int("core.gvfs", value, &core_gvfs_is_bool);
+	return 0;
+}
+
+void gvfs_load_config_value(const char *value)
+{
+	if (value)
+		core_gvfs = git_config_bool_or_int("core.gvfs", value, &core_gvfs_is_bool);
+	else if (startup_info->have_repository == 0)
+		read_early_config(early_core_gvfs_config, NULL);
+	else
+		git_config_get_bool_or_int("core.gvfs", &core_gvfs_is_bool, &core_gvfs);
+
+	/* Turn on all bits if a bool was set in the settings */
+	if (core_gvfs_is_bool && core_gvfs)
+		core_gvfs = -1;
+}
+
+int gvfs_config_is_set(int mask)
+{
+	if (!gvfs_config_loaded)
+		gvfs_load_config_value(0);
+
+	gvfs_config_loaded = 1;
+	return (core_gvfs & mask) == mask;
+}
diff --git a/gvfs.h b/gvfs.h
index 2d6de575bf4a65..e193502151467a 100644
--- a/gvfs.h
+++ b/gvfs.h
@@ -1,8 +1,6 @@
 #ifndef GVFS_H
 #define GVFS_H
 
-#include "cache.h"
-#include "config.h"
 
 /*
  * This file is for the specific settings and methods
@@ -14,37 +12,13 @@
  * The list of bits in the core_gvfs setting
  */
 #define GVFS_SKIP_SHA_ON_INDEX                      (1 << 0)
+#define GVFS_BLOCK_COMMANDS                         (1 << 1)
 #define GVFS_MISSING_OK                             (1 << 2)
 #define GVFS_NO_DELETE_OUTSIDE_SPARSECHECKOUT       (1 << 3)
 #define GVFS_FETCH_SKIP_REACHABILITY_AND_UPLOADPACK (1 << 4)
 #define GVFS_BLOCK_FILTERS_AND_EOL_CONVERSIONS      (1 << 6)
 
-static inline int gvfs_config_is_set(int mask) {
-	return (core_gvfs & mask) == mask;
-}
-
-static inline int gvfs_config_is_set_any(void) {
-	return core_gvfs > 0;
-}
-
-static inline void gvfs_load_config_value(const char *value) {
-	int is_bool = 0;
-
-	if (value)
-		core_gvfs = git_config_bool_or_int("core.gvfs", value, &is_bool);
-	else
-		git_config_get_bool_or_int("core.gvfs", &is_bool, &core_gvfs);
-
-	/* Turn on all bits if a bool was set in the settings */
-	if (is_bool && core_gvfs)
-		core_gvfs = -1;
-}
-
-
-static inline int gvfs_config_load_and_is_set(int mask) {
-	gvfs_load_config_value(0);
-	return gvfs_config_is_set(mask);
-}
-
+void gvfs_load_config_value(const char *value);
+int gvfs_config_is_set(int mask);
 
 #endif /* GVFS_H */
diff --git a/help.c b/help.c
index 919cbb9206aedf..7b7cd2fee83ac7 100644
--- a/help.c
+++ b/help.c
@@ -722,3 +722,19 @@ NORETURN void help_unknown_ref(const char *ref, const char *cmd,
 	string_list_clear(&suggested_refs, 0);
 	exit(1);
 }
+
+int cmd_update(int argc, const char **argv, const char *prefix)
+{
+	const char * const usage[] = {
+		N_("git update-git-for-windows [<options>]\n"
+		   "\t(not supported in this build of Git for Windows)"),
+		NULL
+	};
+	struct option options[] = {
+		OPT_END()
+	};
+
+	argc = parse_options(argc, argv, prefix, options, usage, 0);
+
+	die(_("git %s is not supported in VFSforGit"), argv[0]);
+}
diff --git a/merge-recursive.c b/merge-recursive.c
index 8b669e5f26cf4a..beaf3722bb4819 100644
--- a/merge-recursive.c
+++ b/merge-recursive.c
@@ -1500,7 +1500,7 @@ static int handle_change_delete(struct merge_options *opt,
 		 * path.  We could call update_file_flags() with update_cache=0
 		 * and update_wd=0, but that's a no-op.
 		 */
-		if (change_branch != opt->branch1 || alt_path)
+		if (change_branch != opt->branch1 || alt_path || !file_exists(update_path))
 			ret = update_file(opt, 0, changed, update_path);
 	}
 	free(alt_path);
diff --git a/run-command.c b/run-command.c
index afcda96f1d0ffa..fdb7d70c17b9d4 100644
--- a/run-command.c
+++ b/run-command.c
@@ -7,6 +7,7 @@
 #include "strbuf.h"
 #include "string-list.h"
 #include "quote.h"
+#include "config.h"
 
 void child_process_init(struct child_process *child)
 {
@@ -1309,12 +1310,69 @@ int async_with_fork(void)
 #endif
 }
 
+static int early_hooks_path_config(const char *var, const char *value, void *data)
+{
+	if (!strcmp(var, "core.hookspath"))
+		return git_config_pathname((const char **)data, var, value);
+
+	return 0;
+}
+
+/* Discover the hook before setup_git_directory() was called */
+static const char *hook_path_early(const char *name, struct strbuf *result)
+{
+	static struct strbuf hooks_dir = STRBUF_INIT;
+	static int initialized;
+
+	if (initialized < 0)
+		return NULL;
+
+	if (!initialized) {
+		struct strbuf gitdir = STRBUF_INIT, commondir = STRBUF_INIT;
+		const char *early_hooks_dir = NULL;
+
+		if (discover_git_directory(&commondir, &gitdir) < 0) {
+			initialized = -1;
+			return NULL;
+		}
+
+		read_early_config(early_hooks_path_config, &early_hooks_dir);
+		if (!early_hooks_dir)
+			strbuf_addf(&hooks_dir, "%s/hooks/", commondir.buf);
+		else {
+			strbuf_add_absolute_path(&hooks_dir, early_hooks_dir);
+			strbuf_addch(&hooks_dir, '/');
+		}
+
+		strbuf_release(&gitdir);
+		strbuf_release(&commondir);
+
+		initialized = 1;
+	}
+
+	strbuf_addf(result, "%s%s", hooks_dir.buf, name);
+	return result->buf;
+}
+
 const char *find_hook(const char *name)
 {
 	static struct strbuf path = STRBUF_INIT;
 
 	strbuf_reset(&path);
-	strbuf_git_path(&path, "hooks/%s", name);
+	if (have_git_dir()) {
+		static int forced_config;
+
+		if (!forced_config) {
+			if (!git_hooks_path)
+				git_config_get_pathname("core.hookspath",
+							&git_hooks_path);
+			forced_config = 1;
+		}
+
+		strbuf_git_path(&path, "hooks/%s", name);
+	} else if (!hook_path_early(name, &path))
+		return NULL;
+
 	if (access(path.buf, X_OK) < 0) {
 		int err = errno;
 
diff --git a/send-pack.c b/send-pack.c
index 041712e6295791..ca2cf373e0bcb7 100644
--- a/send-pack.c
+++ b/send-pack.c
@@ -2,6 +2,7 @@
 #include "config.h"
 #include "commit.h"
 #include "refs.h"
+#include "gvfs.h"
 #include "object-store.h"
 #include "pkt-line.h"
 #include "sideband.h"
@@ -51,7 +52,7 @@ static int send_pack_config(const char *var, const char *value, void *unused)
 
 static void feed_object(const struct object_id *oid, FILE *fh, int negative)
 {
-	if (negative &&
+	if (negative && !gvfs_config_is_set(GVFS_MISSING_OK) &&
 	    !has_object_file_with_flags(oid,
 					OBJECT_INFO_SKIP_FETCH_OBJECT |
 					OBJECT_INFO_QUICK))
diff --git a/t/t0021-conversion.sh b/t/t0021-conversion.sh
index 75e5d77435b4f8..75940df651c9a5 100755
--- a/t/t0021-conversion.sh
+++ b/t/t0021-conversion.sh
@@ -328,6 +328,10 @@ test_expect_success "filter: smudge filters blocked when under GVFS" '
 	test_config filter.empty-in-repo.smudge "echo smudged && cat" &&
 	test_config core.gvfs 64 &&
 
+	test_must_fail git checkout &&
+
+	# ensure the local core.gvfs setting overwrites the global setting
+	git config --global core.gvfs false &&
 	test_must_fail git checkout
 '
 
diff --git a/t/t0400-pre-command-hook.sh b/t/t0400-pre-command-hook.sh
new file mode 100755
index 00000000000000..f2a9115e299385
--- /dev/null
+++ b/t/t0400-pre-command-hook.sh
@@ -0,0 +1,69 @@
+#!/bin/sh
+
+test_description='pre-command hook'
+
+. ./test-lib.sh
+
+test_expect_success 'with no hook' '
+	echo "first" > file &&
+	git add file &&
+	git commit -m "first"
+'
+
+test_expect_success 'with succeeding hook' '
+	mkdir -p .git/hooks &&
+	write_script .git/hooks/pre-command <<-EOF &&
+	echo "\$*" | sed "s/ --git-pid=[0-9]*//" \
+		>\$(git rev-parse --git-dir)/pre-command.out
+	EOF
+	echo "second" >> file &&
+	git add file &&
+	test "add file" = "$(cat .git/pre-command.out)" &&
+	echo Hello | git hash-object --stdin &&
+	test "hash-object --stdin" = "$(cat .git/pre-command.out)"
+'
+
+test_expect_success 'with failing hook' '
+	write_script .git/hooks/pre-command <<-EOF &&
+	exit 1
+	EOF
+	echo "third" >> file &&
+	test_must_fail git add file &&
+	test_path_is_missing "$(cat .git/pre-command.out)"
+'
+
+test_expect_success 'in a subdirectory' '
+	echo touch i-was-here | write_script .git/hooks/pre-command &&
+	mkdir sub &&
+	(
+		cd sub &&
+		git version
+	) &&
+	test_path_is_file sub/i-was-here
+'
+
+test_expect_success 'in a subdirectory, using an alias' '
+	git reset --hard &&
+	echo "echo \"\$@; \$(pwd)\" >>log" |
+	write_script .git/hooks/pre-command &&
+	mkdir -p sub &&
+	(
+		cd sub &&
+		git -c alias.v="version" v
+	) &&
+	test_path_is_missing log &&
+	test_line_count = 2 sub/log
+'
+
+test_expect_success 'with core.hooksPath' '
+	mkdir -p .git/alternateHooks &&
+	write_script .git/alternateHooks/pre-command <<-EOF &&
+	echo "alternate" >\$(git rev-parse --git-dir)/pre-command.out
+	EOF
+	write_script .git/hooks/pre-command <<-EOF &&
+	echo "original"	>\$(git rev-parse --git-dir)/pre-command.out
+	EOF
+	git -c core.hooksPath=.git/alternateHooks status &&
+	test "alternate" = "$(cat .git/pre-command.out)"
+'
+test_done
diff --git a/t/t0401-post-command-hook.sh b/t/t0401-post-command-hook.sh
new file mode 100755
index 00000000000000..fcbfc4a0c79c1e
--- /dev/null
+++ b/t/t0401-post-command-hook.sh
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+test_description='post-command hook'
+
+. ./test-lib.sh
+
+test_expect_success 'with no hook' '
+	echo "first" > file &&
+	git add file &&
+	git commit -m "first"
+'
+
+test_expect_success 'with succeeding hook' '
+	mkdir -p .git/hooks &&
+	write_script .git/hooks/post-command <<-EOF &&
+	echo "\$*" | sed "s/ --git-pid=[0-9]*//" \
+		>\$(git rev-parse --git-dir)/post-command.out
+	EOF
+	echo "second" >> file &&
+	git add file &&
+	test "add file --exit_code=0" = "$(cat .git/post-command.out)"
+'
+
+test_expect_success 'with failing pre-command hook' '
+	write_script .git/hooks/pre-command <<-EOF &&
+	exit 1
+	EOF
+	echo "third" >> file &&
+	test_must_fail git add file &&
+	test_path_is_missing "$(cat .git/post-command.out)"
+'
+
+test_done
diff --git a/t/t0402-block-command-on-gvfs.sh b/t/t0402-block-command-on-gvfs.sh
new file mode 100755
index 00000000000000..fd30430b09accc
--- /dev/null
+++ b/t/t0402-block-command-on-gvfs.sh
@@ -0,0 +1,46 @@
+#!/bin/sh
+
+test_description='block commands in GVFS repo'
+
+. ./test-lib.sh
+
+not_with_gvfs () {
+    command=$1 &&
+    shift &&
+    test_expect_success "test $command $*" "
+        test_config alias.g4rbled $command &&
+        test_config core.gvfs true &&
+        test_must_fail git $command $* &&
+        test_must_fail git g4rbled $* &&
+        test_unconfig core.gvfs &&
+        test_must_fail git -c core.gvfs=true $command $* &&
+        test_must_fail git -c core.gvfs=true g4rbled $*
+    "
+}
+
+not_with_gvfs fsck
+not_with_gvfs gc
+not_with_gvfs gc --auto
+not_with_gvfs prune
+not_with_gvfs repack
+not_with_gvfs submodule status
+not_with_gvfs update-index --index-version 2
+not_with_gvfs update-index --skip-worktree
+not_with_gvfs update-index --no-skip-worktree
+not_with_gvfs update-index --split-index
+not_with_gvfs worktree list
+
+test_expect_success 'test gc --auto succeeds when disabled via config' '
+	test_config core.gvfs true &&
+	test_config gc.auto 0 &&
+	git gc --auto
+'
+
+test_expect_success 'update-git-for-windows disabled' '
+	test_must_fail git update 2>out &&
+	test_i18ngrep VFS out &&
+	test_must_fail git update-git-for-windows 2>out &&
+	test_i18ngrep VFS out
+'
+
+test_done
diff --git a/t/t7114-reset-sparse-checkout.sh b/t/t7114-reset-sparse-checkout.sh
new file mode 100755
index 00000000000000..c46cbdb64e4ebc
--- /dev/null
+++ b/t/t7114-reset-sparse-checkout.sh
@@ -0,0 +1,58 @@
+#!/bin/sh
+
+test_description='reset when using a sparse-checkout'
+
+. ./test-lib.sh
+
+# reset using a sparse-checkout file
+
+test_expect_success 'setup' '
+	test_tick &&
+	echo "checkout file" >c &&
+	echo "modify file" >m &&
+	echo "delete file" >d &&
+	git add . &&
+	git commit -m "initial commit" &&
+	echo "added file" >a &&
+	echo "modification of a file" >m &&
+	git rm d &&
+	git add . &&
+	git commit -m "second commit" &&
+	git checkout -b endCommit
+'
+
+test_expect_success 'reset when there is a sparse-checkout' '
+	echo "/c" >.git/info/sparse-checkout &&
+	test_config core.sparsecheckout true &&
+	git checkout -B resetBranch &&
+	test_path_is_missing m &&
+	test_path_is_missing a &&
+	test_path_is_missing d &&
+	git reset HEAD~1 &&
+	test "checkout file" = "$(cat c)" &&
+	test "modification of a file" = "$(cat m)" &&
+	test "added file" = "$(cat a)" &&
+	test_path_is_missing d
+'
+
+test_expect_success 'reset after deleting file without skip-worktree bit' '
+	git checkout -f endCommit &&
+	git clean -xdf &&
+	echo "/c
+/m" >.git/info/sparse-checkout &&
+	test_config core.sparsecheckout true &&
+	git checkout -B resetAfterDelete &&
+	test_path_is_file m &&
+	test_path_is_missing a &&
+	test_path_is_missing d &&
+	rm -f m &&
+	git reset HEAD~1 &&
+	test "checkout file" = "$(cat c)" &&
+	test "added file" = "$(cat a)" &&
+	test_path_is_missing m &&
+	test_path_is_missing d
+'
+
+
+
+test_done
diff --git a/t/t7615-merge-sparse-checkout.sh b/t/t7615-merge-sparse-checkout.sh
new file mode 100755
index 00000000000000..8e8208a61d39eb
--- /dev/null
+++ b/t/t7615-merge-sparse-checkout.sh
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+test_description='merge can handle sparse-checkout'
+
+. ./test-lib.sh
+
+# merges with conflicts
+
+test_expect_success 'setup' '
+	test_commit a &&
+	test_commit file &&
+	git checkout -b delete-file &&
+	git rm file.t &&
+	test_tick &&
+	git commit -m "remove file" &&
+	git checkout master &&
+	test_commit modify file.t changed
+'
+
+test_expect_success 'merge conflict deleted file and modified' '
+	echo "/a.t" >.git/info/sparse-checkout &&
+	test_config core.sparsecheckout true &&
+	git checkout -f &&
+	test_path_is_missing file.t &&
+	test_must_fail git merge delete-file &&
+	test_path_is_file file.t &&
+	test "changed" = "$(cat file.t)"
+'
+
+test_done
diff --git a/unpack-trees.c b/unpack-trees.c
index cf542868c109f2..ecf59a463a94d1 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -543,7 +543,9 @@ static int apply_sparse_checkout(struct index_state *istate,
 			ce->ce_flags &= ~CE_SKIP_WORKTREE;
 			return -1;
 		}
-		ce->ce_flags |= CE_WT_REMOVE;
+		if (!gvfs_config_is_set(GVFS_NO_DELETE_OUTSIDE_SPARSECHECKOUT))
+			ce->ce_flags |= CE_WT_REMOVE;
+
 		ce->ce_flags &= ~CE_UPDATE;
 	}
 	if (was_skip_worktree && !ce_skip_worktree(ce)) {