diff --git a/Documentation/git.txt b/Documentation/git.txt
index 463b0eb0f5..483a1f3547 100644
--- a/Documentation/git.txt
+++ b/Documentation/git.txt
@@ -595,6 +595,10 @@ into it.
 Unsetting the variable, or setting it to empty, "0" or
 "false" (case insensitive) disables trace messages.
 
+`GIT_TRACE_FSMONITOR`::
+	Enables trace messages for the filesystem monitor extension.
+	See `GIT_TRACE` for available trace output options.
+
 `GIT_TRACE_PACK_ACCESS`::
 	Enables trace messages for all accesses to any packs. For each
 	access, the pack file name and an offset in the pack is
diff --git a/cache.h b/cache.h
index 7c71681236..f684c7933b 100644
--- a/cache.h
+++ b/cache.h
@@ -348,6 +348,7 @@ struct index_state {
 	unsigned char sha1[20];
 	struct untracked_cache *untracked;
 	uint64_t fsmonitor_last_update;
+	struct ewah_bitmap *fsmonitor_dirty;
 };
 
 extern struct index_state the_index;
diff --git a/fsmonitor.c b/fsmonitor.c
index 7c1540c054..0af7c4edba 100644
--- a/fsmonitor.c
+++ b/fsmonitor.c
@@ -26,7 +26,6 @@ int read_fsmonitor_extension(struct index_state *istate, const void *data,
 	uint32_t hdr_version;
 	uint32_t ewah_size;
 	struct ewah_bitmap *fsmonitor_dirty;
-	int i;
 	int ret;
 
 	if (sz < sizeof(uint32_t) + sizeof(uint64_t) + sizeof(uint32_t))
@@ -49,31 +48,25 @@ int read_fsmonitor_extension(struct index_state *istate, const void *data,
 		ewah_free(fsmonitor_dirty);
 		return error("failed to parse ewah bitmap reading fsmonitor index extension");
 	}
-
-	if (git_config_get_fsmonitor()) {
-		/* Mark all entries valid */
-		for (i = 0; i < istate->cache_nr; i++)
-			istate->cache[i]->ce_flags |= CE_FSMONITOR_VALID;
-
-		/* Mark all previously saved entries as dirty */
-		ewah_each_bit(fsmonitor_dirty, fsmonitor_ewah_callback, istate);
-
-		/* Now mark the untracked cache for fsmonitor usage */
-		if (istate->untracked)
-			istate->untracked->use_fsmonitor = 1;
-	}
-	ewah_free(fsmonitor_dirty);
+	istate->fsmonitor_dirty = fsmonitor_dirty;
 
 	trace_printf_key(&trace_fsmonitor, "read fsmonitor extension successful");
 	return 0;
 }
 
+void fill_fsmonitor_bitmap(struct index_state *istate)
+{
+	int i;
+	istate->fsmonitor_dirty = ewah_new();
+	for (i = 0; i < istate->cache_nr; i++)
+		if (!(istate->cache[i]->ce_flags & CE_FSMONITOR_VALID))
+			ewah_set(istate->fsmonitor_dirty, i);
+}
+
 void write_fsmonitor_extension(struct strbuf *sb, struct index_state *istate)
 {
 	uint32_t hdr_version;
 	uint64_t tm;
-	struct ewah_bitmap *bitmap;
-	int i;
 	uint32_t ewah_start;
 	uint32_t ewah_size = 0;
 	int fixup = 0;
@@ -87,12 +80,9 @@ void write_fsmonitor_extension(struct strbuf *sb, struct index_state *istate)
 	strbuf_add(sb, &ewah_size, sizeof(uint32_t)); /* we'll fix this up later */
 
 	ewah_start = sb->len;
-	bitmap = ewah_new();
-	for (i = 0; i < istate->cache_nr; i++)
-		if (!(istate->cache[i]->ce_flags & CE_FSMONITOR_VALID))
-			ewah_set(bitmap, i);
-	ewah_serialize_strbuf(bitmap, sb);
-	ewah_free(bitmap);
+	ewah_serialize_strbuf(istate->fsmonitor_dirty, sb);
+	ewah_free(istate->fsmonitor_dirty);
+	istate->fsmonitor_dirty = NULL;
 
 	/* fix up size field */
 	put_be32(&ewah_size, sb->len - ewah_start);
@@ -121,6 +111,7 @@ static int query_fsmonitor(int version, uint64_t last_update, struct strbuf *que
 	argv[3] = NULL;
 	cp.argv = argv;
 	cp.use_shell = 1;
+	cp.dir = get_git_work_tree();
 
 	return capture_command(&cp, query_result, 1024);
 }
@@ -238,7 +229,29 @@ void remove_fsmonitor(struct index_state *istate)
 
 void tweak_fsmonitor(struct index_state *istate)
 {
-	switch (git_config_get_fsmonitor()) {
+	int i;
+	int fsmonitor_enabled = git_config_get_fsmonitor();
+
+	if (istate->fsmonitor_dirty) {
+		if (fsmonitor_enabled) {
+			/* Mark all entries valid */
+			for (i = 0; i < istate->cache_nr; i++) {
+				istate->cache[i]->ce_flags |= CE_FSMONITOR_VALID;
+			}
+
+			/* Mark all previously saved entries as dirty */
+			ewah_each_bit(istate->fsmonitor_dirty, fsmonitor_ewah_callback, istate);
+
+			/* Now mark the untracked cache for fsmonitor usage */
+			if (istate->untracked)
+				istate->untracked->use_fsmonitor = 1;
+		}
+
+		ewah_free(istate->fsmonitor_dirty);
+		istate->fsmonitor_dirty = NULL;
+	}
+
+	switch (fsmonitor_enabled) {
 	case -1: /* keep: do nothing */
 		break;
 	case 0: /* false */
diff --git a/fsmonitor.h b/fsmonitor.h
index 0de644e01a..cd3cc0ccf2 100644
--- a/fsmonitor.h
+++ b/fsmonitor.h
@@ -10,7 +10,14 @@ extern struct trace_key trace_fsmonitor;
 extern int read_fsmonitor_extension(struct index_state *istate, const void *data, unsigned long sz);
 
 /*
- * Write the CE_FSMONITOR_VALID state into the fsmonitor index extension.
+ * Fill the fsmonitor_dirty ewah bits with their state from the index,
+ * before it is split during writing.
+ */
+extern void fill_fsmonitor_bitmap(struct index_state *istate);
+
+/*
+ * Write the CE_FSMONITOR_VALID state into the fsmonitor index
+ * extension.  Reads from the fsmonitor_dirty ewah in the index.
  */
 extern void write_fsmonitor_extension(struct strbuf *sb, struct index_state *istate);
 
diff --git a/read-cache.c b/read-cache.c
index 87e88b2642..fbb4967c81 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -2535,6 +2535,9 @@ int write_locked_index(struct index_state *istate, struct lock_file *lock,
 	int new_shared_index, ret;
 	struct split_index *si = istate->split_index;
 
+	if (istate->fsmonitor_last_update)
+		fill_fsmonitor_bitmap(istate);
+
 	if (!si || alternate_index_output ||
 	    (istate->cache_changed & ~EXTMASK)) {
 		if (si)
diff --git a/t/t7519-status-fsmonitor.sh b/t/t7519-status-fsmonitor.sh
index c6df85af5e..eb2d13bbcf 100755
--- a/t/t7519-status-fsmonitor.sh
+++ b/t/t7519-status-fsmonitor.sh
@@ -301,4 +301,17 @@ do
 	done
 done
 
+# test that splitting the index dosn't interfere
+test_expect_success 'splitting the index results in the same state' '
+	write_integration_script &&
+	dirty_repo &&
+	git update-index --fsmonitor  &&
+	git ls-files -f >expect &&
+	test-dump-fsmonitor >&2 && echo &&
+	git update-index --fsmonitor --split-index &&
+	test-dump-fsmonitor >&2 && echo &&
+	git ls-files -f >actual &&
+	test_cmp expect actual
+'
+
 test_done
diff --git a/t/t7519/fsmonitor-watchman b/t/t7519/fsmonitor-watchman
index a3e30bf54f..5514edcf68 100755
--- a/t/t7519/fsmonitor-watchman
+++ b/t/t7519/fsmonitor-watchman
@@ -29,19 +29,13 @@ if ($version == 1) {
 	    "Falling back to scanning...\n";
 }
 
-# Convert unix style paths to escaped Windows style paths when running
-# in Windows command prompt
-
-my $system = `uname -s`;
-$system =~ s/[\r\n]+//g;
 my $git_work_tree;
-
-if ($system =~ m/^MSYS_NT/ || $system =~ m/^MINGW/) {
-	$git_work_tree = `cygpath -aw "\$PWD"`;
-	$git_work_tree =~ s/[\r\n]+//g;
-	$git_work_tree =~ s,\\,/,g;
+if ($^O =~ 'msys' || $^O =~ 'cygwin') {
+	$git_work_tree = Win32::GetCwd();
+	$git_work_tree =~ tr/\\/\//;
 } else {
-	$git_work_tree = $ENV{'PWD'};
+	require Cwd;
+	$git_work_tree = Cwd::cwd();
 }
 
 my $retry = 1;
diff --git a/templates/hooks--fsmonitor-watchman.sample b/templates/hooks--fsmonitor-watchman.sample
index 9eba8a7409..e673bb3980 100755
--- a/templates/hooks--fsmonitor-watchman.sample
+++ b/templates/hooks--fsmonitor-watchman.sample
@@ -28,19 +28,13 @@ if ($version == 1) {
 	    "Falling back to scanning...\n";
 }
 
-# Convert unix style paths to escaped Windows style paths when running
-# in Windows command prompt
-
-my $system = `uname -s`;
-$system =~ s/[\r\n]+//g;
 my $git_work_tree;
-
-if ($system =~ m/^MSYS_NT/ || $system =~ m/^MINGW/) {
-	$git_work_tree = `cygpath -aw "\$PWD"`;
-	$git_work_tree =~ s/[\r\n]+//g;
-	$git_work_tree =~ s,\\,/,g;
+if ($^O =~ 'msys' || $^O =~ 'cygwin') {
+	$git_work_tree = Win32::GetCwd();
+	$git_work_tree =~ tr/\\/\//;
 } else {
-	$git_work_tree = $ENV{'PWD'};
+	require Cwd;
+	$git_work_tree = Cwd::cwd();
 }
 
 my $retry = 1;
@@ -49,7 +43,7 @@ launch_watchman();
 
 sub launch_watchman {
 
-	my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j')
+	my $pid = open2(\*CHLD_OUT, \*CHLD_IN, 'watchman -j --no-pretty')
 	    or die "open2() failed: $!\n" .
 	    "Falling back to scanning...\n";