diff --git a/git-gui.sh b/git-gui.sh
index 03c450d73f06574381b2a2dc8e765237fbcfc03e..4085e8fea59f2b819812f20185df89379d851c0b 100755
--- a/git-gui.sh
+++ b/git-gui.sh
@@ -1059,6 +1059,7 @@ set current_branch {}
 set is_detached 0
 set current_diff_path {}
 set is_3way_diff 0
+set is_conflict_diff 0
 set selected_commit_type new
 
 set nullid "0000000000000000000000000000000000000000"
@@ -2078,19 +2079,21 @@ proc toggle_or_diff {w x y} {
 	$ui_index tag remove in_sel 0.0 end
 	$ui_workdir tag remove in_sel 0.0 end
 
-	# Do not stage files with conflicts
+	# Determine the state of the file
 	if {[info exists file_states($path)]} {
 		set state [lindex $file_states($path) 0]
 	} else {
 		set state {__}
 	}
 
-	if {[string first {U} $state] >= 0} {
-		set col 1
-	}
-
 	# Restage the file, or simply show the diff
 	if {$col == 0 && $y > 1} {
+		# Conflicts need special handling
+		if {[string first {U} $state] >= 0} {
+			merge_stage_workdir $path $w $lno
+			return
+		}
+
 		if {[string index $state 1] eq {O}} {
 			set mmask {}
 		} else {
@@ -3057,11 +3060,6 @@ $ctxmmg add command \
 	-command {merge_resolve_one 1}
 lappend diff_actions [list $ctxmmg entryconf [$ctxmmg index last] -state]
 $ctxmmg add separator
-$ctxmmg add command \
-	-label [mc "Stage Working Copy"] \
-	-command {merge_resolve_one 0}
-lappend diff_actions [list $ctxmmg entryconf [$ctxmmg index last] -state]
-$ctxmmg add separator
 create_common_diff_popup $ctxmmg
 
 proc popup_diff_menu {ctxm ctxmmg x y X Y} {
diff --git a/lib/diff.tcl b/lib/diff.tcl
index b61629676f69a4bcb5c6a42af72e0c82a69cea73..abe502d97104cb62bed308b0f5025c9d014834fb 100644
--- a/lib/diff.tcl
+++ b/lib/diff.tcl
@@ -69,9 +69,9 @@ A rescan will be automatically started to find other files which may have the sa
 	rescan ui_ready 0
 }
 
-proc show_diff {path w {lno {}} {scroll_pos {}}} {
+proc show_diff {path w {lno {}} {scroll_pos {}} {callback {}}} {
 	global file_states file_lists
-	global is_3way_diff diff_active repo_config
+	global is_3way_diff is_conflict_diff diff_active repo_config
 	global ui_diff ui_index ui_workdir
 	global current_diff_path current_diff_side current_diff_header
 	global current_diff_queue
@@ -92,36 +92,42 @@ proc show_diff {path w {lno {}} {scroll_pos {}}} {
 
 	set s $file_states($path)
 	set m [lindex $s 0]
+	set is_conflict_diff 0
 	set current_diff_path $path
 	set current_diff_side $w
 	set current_diff_queue {}
 	ui_status [mc "Loading diff of %s..." [escape_path $path]]
 
+	set cont_info [list $scroll_pos $callback]
+
 	if {[string first {U} $m] >= 0} {
-		merge_load_stages $path [list show_unmerged_diff $scroll_pos]
+		merge_load_stages $path [list show_unmerged_diff $cont_info]
 	} elseif {$m eq {_O}} {
-		show_other_diff $path $w $m $scroll_pos
+		show_other_diff $path $w $m $cont_info
 	} else {
-		start_show_diff $scroll_pos
+		start_show_diff $cont_info
 	}
 }
 
-proc show_unmerged_diff {scroll_pos} {
+proc show_unmerged_diff {cont_info} {
 	global current_diff_path current_diff_side
-	global merge_stages ui_diff
+	global merge_stages ui_diff is_conflict_diff
 	global current_diff_queue
 
 	if {$merge_stages(2) eq {}} {
+		set is_conflict_diff 1
 		lappend current_diff_queue \
 			[list "LOCAL: deleted\nREMOTE:\n" d======= \
 			    [list ":1:$current_diff_path" ":3:$current_diff_path"]]
 	} elseif {$merge_stages(3) eq {}} {
+		set is_conflict_diff 1
 		lappend current_diff_queue \
 			[list "REMOTE: deleted\nLOCAL:\n" d======= \
 			    [list ":1:$current_diff_path" ":2:$current_diff_path"]]
 	} elseif {[lindex $merge_stages(1) 0] eq {120000}
 		|| [lindex $merge_stages(2) 0] eq {120000}
 		|| [lindex $merge_stages(3) 0] eq {120000}} {
+		set is_conflict_diff 1
 		lappend current_diff_queue \
 			[list "LOCAL:\n" d======= \
 			    [list ":1:$current_diff_path" ":2:$current_diff_path"]]
@@ -129,14 +135,14 @@ proc show_unmerged_diff {scroll_pos} {
 			[list "REMOTE:\n" d======= \
 			    [list ":1:$current_diff_path" ":3:$current_diff_path"]]
 	} else {
-		start_show_diff $scroll_pos
+		start_show_diff $cont_info
 		return
 	}
 
-	advance_diff_queue $scroll_pos
+	advance_diff_queue $cont_info
 }
 
-proc advance_diff_queue {scroll_pos} {
+proc advance_diff_queue {cont_info} {
 	global current_diff_queue ui_diff
 
 	set item [lindex $current_diff_queue 0]
@@ -146,10 +152,10 @@ proc advance_diff_queue {scroll_pos} {
 	$ui_diff insert end [lindex $item 0] [lindex $item 1]
 	$ui_diff conf -state disabled
 
-	start_show_diff $scroll_pos [lindex $item 2]
+	start_show_diff $cont_info [lindex $item 2]
 }
 
-proc show_other_diff {path w m scroll_pos} {
+proc show_other_diff {path w m cont_info} {
 	global file_states file_lists
 	global is_3way_diff diff_active repo_config
 	global ui_diff ui_index ui_workdir
@@ -228,16 +234,21 @@ proc show_other_diff {path w m scroll_pos} {
 		$ui_diff conf -state disabled
 		set diff_active 0
 		unlock_index
+		set scroll_pos [lindex $cont_info 0]
 		if {$scroll_pos ne {}} {
 			update
 			$ui_diff yview moveto $scroll_pos
 		}
 		ui_ready
+		set callback [lindex $cont_info 1]
+		if {$callback ne {}} {
+			eval $callback
+		}
 		return
 	}
 }
 
-proc start_show_diff {scroll_pos {add_opts {}}} {
+proc start_show_diff {cont_info {add_opts {}}} {
 	global file_states file_lists
 	global is_3way_diff diff_active repo_config
 	global ui_diff ui_index ui_workdir
@@ -292,12 +303,12 @@ proc start_show_diff {scroll_pos {add_opts {}}} {
 		-blocking 0 \
 		-encoding [get_path_encoding $path] \
 		-translation lf
-	fileevent $fd readable [list read_diff $fd $scroll_pos]
+	fileevent $fd readable [list read_diff $fd $cont_info]
 }
 
-proc read_diff {fd scroll_pos} {
+proc read_diff {fd cont_info} {
 	global ui_diff diff_active
-	global is_3way_diff current_diff_header
+	global is_3way_diff is_conflict_diff current_diff_header
 	global current_diff_queue
 
 	$ui_diff conf -state normal
@@ -345,6 +356,7 @@ proc read_diff {fd scroll_pos} {
 			{--} {set tags d_--}
 			{++} {
 				if {[regexp {^\+\+([<>]{7} |={7})} $line _g op]} {
+					set is_conflict_diff 1
 					set line [string replace $line 0 1 {  }]
 					set tags d$op
 				} else {
@@ -364,6 +376,7 @@ proc read_diff {fd scroll_pos} {
 			{-} {set tags d_-}
 			{+} {
 				if {[regexp {^\+([<>]{7} |={7})} $line _g op]} {
+					set is_conflict_diff 1
 					set line [string replace $line 0 0 { }]
 					set tags d$op
 				} else {
@@ -388,12 +401,13 @@ proc read_diff {fd scroll_pos} {
 		close $fd
 
 		if {$current_diff_queue ne {}} {
-			advance_diff_queue $scroll_pos
+			advance_diff_queue $cont_info
 			return
 		}
 
 		set diff_active 0
 		unlock_index
+		set scroll_pos [lindex $cont_info 0]
 		if {$scroll_pos ne {}} {
 			update
 			$ui_diff yview moveto $scroll_pos
@@ -403,6 +417,10 @@ proc read_diff {fd scroll_pos} {
 		if {[$ui_diff index end] eq {2.0}} {
 			handle_empty_diff
 		}
+		set callback [lindex $cont_info 1]
+		if {$callback ne {}} {
+			eval $callback
+		}
 	}
 }
 
diff --git a/lib/mergetool.tcl b/lib/mergetool.tcl
index a44a7258bccc5bffea21b470eb297b02f0ad97af..6ab5701d937b9a719570907e745609b60d1d56a8 100644
--- a/lib/mergetool.tcl
+++ b/lib/mergetool.tcl
@@ -5,12 +5,6 @@ proc merge_resolve_one {stage} {
 	global current_diff_path
 
 	switch -- $stage {
-		0 {	# Stage without confirmation, to minimize
-			# disruption of the rerere workflow
-			merge_add_resolution $current_diff_path
-			return
-		}
-
 		1 { set targetquestion [mc "Force resolution to the base version?"] }
 		2 { set targetquestion [mc "Force resolution to this branch?"] }
 		3 { set targetquestion [mc "Force resolution to the other branch?"] }
@@ -29,6 +23,33 @@ This operation can be undone only by restarting the merge." \
 	}
 }
 
+proc merge_stage_workdir {path w lno} {
+	global current_diff_path diff_active
+
+	if {$diff_active} return
+
+	if {$path ne $current_diff_path} {
+		show_diff $path $w $lno {} [list do_merge_stage_workdir $path]
+	} else {
+		do_merge_stage_workdir $path
+	}
+}
+
+proc do_merge_stage_workdir {path} {
+	global current_diff_path is_conflict_diff
+
+	if {$path ne $current_diff_path} return;
+
+	if {$is_conflict_diff} {
+		if {[ask_popup [mc "File %s seems to have unresolved conflicts, still stage?" \
+				[short_path $path]]] ne {yes}} {
+			return
+		}
+	}
+
+	merge_add_resolution $path
+}
+
 proc merge_add_resolution {path} {
 	global current_diff_path ui_workdir