diff --git a/git-gui/git-gui.sh b/git-gui/git-gui.sh
index 29a790e481..fa30ccc5d6 100755
--- a/git-gui/git-gui.sh
+++ b/git-gui/git-gui.sh
@@ -60,54 +60,6 @@ if {![catch {set _verbose $env(GITGUI_VERBOSE)}]} {
 	}
 }
 
-######################################################################
-##
-## configure our library
-
-set oguilib {@@GITGUI_LIBDIR@@}
-set oguirel {@@GITGUI_RELATIVE@@}
-if {$oguirel eq {1}} {
-	set oguilib [file dirname [file dirname [file normalize $argv0]]]
-	set oguilib [file join $oguilib share git-gui lib]
-} elseif {[string match @@* $oguirel]} {
-	set oguilib [file join [file dirname [file normalize $argv0]] lib]
-}
-
-set idx [file join $oguilib tclIndex]
-if {[catch {set fd [open $idx r]} err]} {
-	catch {wm withdraw .}
-	tk_messageBox \
-		-icon error \
-		-type ok \
-		-title "git-gui: fatal error" \
-		-message $err
-	exit 1
-}
-if {[gets $fd] eq {# Autogenerated by git-gui Makefile}} {
-	set idx [list]
-	while {[gets $fd n] >= 0} {
-		if {$n ne {} && ![string match #* $n]} {
-			lappend idx $n
-		}
-	}
-} else {
-	set idx {}
-}
-close $fd
-
-if {$idx ne {}} {
-	set loaded [list]
-	foreach p $idx {
-		if {[lsearch -exact $loaded $p] >= 0} continue
-		source [file join $oguilib $p]
-		lappend loaded $p
-	}
-	unset loaded p
-} else {
-	set auto_path [concat [list $oguilib] $auto_path]
-}
-unset -nocomplain oguirel idx fd
-
 ######################################################################
 ##
 ## read only globals
@@ -532,7 +484,11 @@ if {$_git eq {}} {
 
 if {[catch {set _git_version [git --version]} err]} {
 	catch {wm withdraw .}
-	error_popup "Cannot determine Git version:
+	tk_messageBox \
+		-icon error \
+		-type ok \
+		-title "git-gui: fatal error" \
+		-message "Cannot determine Git version:
 
 $err
 
@@ -541,7 +497,11 @@ $err
 }
 if {![regsub {^git version } $_git_version {} _git_version]} {
 	catch {wm withdraw .}
-	error_popup "Cannot parse Git version string:\n\n$_git_version"
+	tk_messageBox \
+		-icon error \
+		-type ok \
+		-title "git-gui: fatal error" \
+		-message "Cannot parse Git version string:\n\n$_git_version"
 	exit 1
 }
 
@@ -619,7 +579,11 @@ proc git-version {args} {
 
 if {[git-version < 1.5]} {
 	catch {wm withdraw .}
-	error_popup "[appname] requires Git 1.5.0 or later.
+	tk_messageBox \
+		-icon error \
+		-type ok \
+		-title "git-gui: fatal error" \
+		-message "[appname] requires Git 1.5.0 or later.
 
 You are using [git-version]:
 
@@ -627,6 +591,54 @@ You are using [git-version]:
 	exit 1
 }
 
+######################################################################
+##
+## configure our library
+
+set oguilib {@@GITGUI_LIBDIR@@}
+set oguirel {@@GITGUI_RELATIVE@@}
+if {$oguirel eq {1}} {
+	set oguilib [file dirname [file dirname [file normalize $argv0]]]
+	set oguilib [file join $oguilib share git-gui lib]
+} elseif {[string match @@* $oguirel]} {
+	set oguilib [file join [file dirname [file normalize $argv0]] lib]
+}
+
+set idx [file join $oguilib tclIndex]
+if {[catch {set fd [open $idx r]} err]} {
+	catch {wm withdraw .}
+	tk_messageBox \
+		-icon error \
+		-type ok \
+		-title "git-gui: fatal error" \
+		-message $err
+	exit 1
+}
+if {[gets $fd] eq {# Autogenerated by git-gui Makefile}} {
+	set idx [list]
+	while {[gets $fd n] >= 0} {
+		if {$n ne {} && ![string match #* $n]} {
+			lappend idx $n
+		}
+	}
+} else {
+	set idx {}
+}
+close $fd
+
+if {$idx ne {}} {
+	set loaded [list]
+	foreach p $idx {
+		if {[lsearch -exact $loaded $p] >= 0} continue
+		source [file join $oguilib $p]
+		lappend loaded $p
+	}
+	unset loaded p
+} else {
+	set auto_path [concat [list $oguilib] $auto_path]
+}
+unset -nocomplain oguirel idx fd
+
 ######################################################################
 ##
 ## feature option selection
@@ -691,7 +703,15 @@ if {![file isdirectory $_gitdir]} {
 	error_popup "Git directory not found:\n\n$_gitdir"
 	exit 1
 }
-if {![is_enabled bare]} {
+if {$_prefix ne {}} {
+	regsub -all {[^/]+/} $_prefix ../ cdup
+	if {[catch {cd $cdup} err]} {
+		catch {wm withdraw .}
+		error_popup "Cannot move to top of working directory:\n\n$err"
+		exit 1
+	}
+	unset cdup
+} elseif {![is_enabled bare]} {
 	if {[lindex [file split $_gitdir] end] ne {.git}} {
 		catch {wm withdraw .}
 		error_popup "Cannot use funny .git directory:\n\n$_gitdir"
@@ -726,6 +746,7 @@ set empty_tree {}
 set current_branch {}
 set is_detached 0
 set current_diff_path {}
+set is_3way_diff 0
 set selected_commit_type new
 
 ######################################################################
@@ -1936,6 +1957,12 @@ if {$browser ne {}} {
 }
 unset browser doc_path doc_url
 
+set root_exists 0
+bind . <Visibility> {
+	bind . <Visibility> {}
+	set root_exists 1
+}
+
 # -- Standard bindings
 #
 wm protocol . WM_DELETE_WINDOW do_quit
@@ -2410,23 +2437,26 @@ $ctxm add separator
 $ctxm add command -label {Options...} \
 	-command do_options
 proc popup_diff_menu {ctxm x y X Y} {
-	global current_diff_path
+	global current_diff_path file_states
 	set ::cursorX $x
 	set ::cursorY $y
 	if {$::ui_index eq $::current_diff_side} {
-		$ctxm entryconf $::ui_diff_applyhunk \
-			-state normal \
-			-label {Unstage Hunk From Commit}
-	} elseif {![info exists file_states($current_diff_path)]
-		|| {_O} eq [lindex $file_states($::current_diff_path) 0]} {
-		$ctxm entryconf $::ui_diff_applyhunk \
-			-state disabled \
-			-label {Stage Hunk For Commit}
+		set s normal
+		set l "Unstage Hunk From Commit"
 	} else {
-		$ctxm entryconf $::ui_diff_applyhunk \
-			-state normal \
-			-label {Stage Hunk For Commit}
+		if {$current_diff_path eq {}
+			|| ![info exists file_states($current_diff_path)]
+			|| {_O} eq [lindex $file_states($current_diff_path) 0]} {
+			set s disabled
+		} else {
+			set s normal
+		}
+		set l "Stage Hunk For Commit"
 	}
+	if {$::is_3way_diff} {
+		set s disabled
+	}
+	$ctxm entryconf $::ui_diff_applyhunk -state $s -label $l
 	tk_popup $ctxm $X $Y
 }
 bind_button3 $ui_diff [list popup_diff_menu $ctxm %x %y %X %Y]
diff --git a/git-gui/lib/class.tcl b/git-gui/lib/class.tcl
index 24e8cecea4..dc2141192a 100644
--- a/git-gui/lib/class.tcl
+++ b/git-gui/lib/class.tcl
@@ -148,11 +148,12 @@ proc make_toplevel {t w args} {
 		}
 	}
 
-	if {[winfo ismapped .]} {
+	if {$::root_exists || [winfo ismapped .]} {
 		regsub -all {::} $this {__} w
 		set top .$w
 		set pfx $top
 		toplevel $top
+		set ::root_exists 1
 	} else {
 		set top .
 		set pfx {}
diff --git a/git-gui/lib/merge.tcl b/git-gui/lib/merge.tcl
index 5de0d82b14..0e50919d4c 100644
--- a/git-gui/lib/merge.tcl
+++ b/git-gui/lib/merge.tcl
@@ -114,7 +114,7 @@ method _start {} {
 	lappend cmd --strategy=recursive
 	lappend cmd [git fmt-merge-msg <[gitdir FETCH_HEAD]]
 	lappend cmd HEAD
-	lappend cmd $cmit
+	lappend cmd $name
 
 	set msg "Merging $current_branch and $stitle"
 	ui_status "$msg..."