diff --git a/IkiWiki/Plugin/aggregate.pm b/IkiWiki/Plugin/aggregate.pm
index 5e22609c9..83bd670cb 100644
--- a/IkiWiki/Plugin/aggregate.pm
+++ b/IkiWiki/Plugin/aggregate.pm
@@ -201,7 +201,7 @@ sub migrate_to_internal {
 		if (-e $oldoutput) {
 			require IkiWiki::Render;
 			debug("removing output file $oldoutput");
-			IkiWiki::prune($oldoutput);
+			IkiWiki::prune($oldoutput, $config{destdir});
 		}
 	}
 	
diff --git a/IkiWiki/Plugin/amazon_s3.pm b/IkiWiki/Plugin/amazon_s3.pm
index cfd8cd347..a9da6bf12 100644
--- a/IkiWiki/Plugin/amazon_s3.pm
+++ b/IkiWiki/Plugin/amazon_s3.pm
@@ -232,8 +232,9 @@ sub writefile ($$$;$$) {
 }
 
 # This is a wrapper around the real prune.
-sub prune ($) {
+sub prune ($;$) {
 	my $file=shift;
+	my $up_to=shift;
 
 	my @keys=IkiWiki::Plugin::amazon_s3::file2keys($file);
 
@@ -250,7 +251,7 @@ sub prune ($) {
 		}
 	}
 
-	return $IkiWiki::Plugin::amazon_s3::subs{'IkiWiki::prune'}->($file);
+	return $IkiWiki::Plugin::amazon_s3::subs{'IkiWiki::prune'}->($file, $up_to);
 }
 
 1
diff --git a/IkiWiki/Plugin/attachment.pm b/IkiWiki/Plugin/attachment.pm
index 133a54daf..aea70429d 100644
--- a/IkiWiki/Plugin/attachment.pm
+++ b/IkiWiki/Plugin/attachment.pm
@@ -286,7 +286,7 @@ sub attachments_save {
 	}
 	return unless @attachments;
 	require IkiWiki::Render;
-	IkiWiki::prune($dir);
+	IkiWiki::prune($dir, $config{wikistatedir}."/attachments");
 
 	# Check the attachments in and trigger a wiki refresh.
 	if ($config{rcs}) {
diff --git a/IkiWiki/Plugin/comments.pm b/IkiWiki/Plugin/comments.pm
index 0d5e3c078..4bf8ae469 100644
--- a/IkiWiki/Plugin/comments.pm
+++ b/IkiWiki/Plugin/comments.pm
@@ -665,9 +665,11 @@ sub commentmoderation ($$) {
 
 				my $page=IkiWiki::dirname($f);
 				my $file="$config{srcdir}/$f";
+				my $filedir="$config{srcdir}";
 				if (! -e $file) {
 					# old location
 					$file="$config{wikistatedir}/comments_pending/".$f;
+					$filedir="$config{wikistatedir}/comments_pending";
 				}
 
 				if ($action eq 'Accept') {
@@ -682,7 +684,7 @@ sub commentmoderation ($$) {
 				}
 
 				require IkiWiki::Render;
-				IkiWiki::prune($file);
+				IkiWiki::prune($file, $filedir);
 			}
 		}
 
diff --git a/IkiWiki/Plugin/editpage.pm b/IkiWiki/Plugin/editpage.pm
index 54051c58c..d3c695935 100644
--- a/IkiWiki/Plugin/editpage.pm
+++ b/IkiWiki/Plugin/editpage.pm
@@ -39,7 +39,7 @@ sub refresh () {
 				}
 				if ($delete) {
 					debug(sprintf(gettext("removing old preview %s"), $file));
-					IkiWiki::prune("$config{destdir}/$file");
+					IkiWiki::prune("$config{destdir}/$file", $config{destdir});
 				}
 			}
 			elsif (defined $mtime) {
diff --git a/IkiWiki/Plugin/po.pm b/IkiWiki/Plugin/po.pm
index 26c6463da..53e6af92f 100644
--- a/IkiWiki/Plugin/po.pm
+++ b/IkiWiki/Plugin/po.pm
@@ -1102,7 +1102,7 @@ sub deletetranslations ($) {
 			IkiWiki::rcs_remove($_);
 		}
 		else {
-			IkiWiki::prune("$config{srcdir}/$_");
+			IkiWiki::prune("$config{srcdir}/$_", $config{srcdir});
 		}
 	} @todelete;
 
diff --git a/IkiWiki/Plugin/remove.pm b/IkiWiki/Plugin/remove.pm
index 14ac01c9b..d48b28f95 100644
--- a/IkiWiki/Plugin/remove.pm
+++ b/IkiWiki/Plugin/remove.pm
@@ -22,6 +22,13 @@ sub getsetup () {
 		},
 }
 
+sub allowed_dirs {
+	return grep { defined $_ } (
+		$config{srcdir},
+		$IkiWiki::Plugin::transient::transientdir,
+	);
+}
+
 sub check_canremove ($$$) {
 	my $page=shift;
 	my $q=shift;
@@ -33,12 +40,22 @@ sub check_canremove ($$$) {
 			htmllink("", "", $page, noimageinline => 1)));
 	}
 
-	# Must exist on disk, and be a regular file.
+	# Must exist in either the srcdir or a suitable underlay (e.g.
+	# transient underlay), and be a regular file.
 	my $file=$pagesources{$page};
-	if (! -e "$config{srcdir}/$file") {
+	my $dir;
+
+	foreach my $srcdir (allowed_dirs()) {
+		if (-e "$srcdir/$file") {
+			$dir = $srcdir;
+			last;
+		}
+	}
+
+	if (! defined $dir) {
 		error(sprintf(gettext("%s is not in the srcdir, so it cannot be deleted"), $file));
 	}
-	elsif (-l "$config{srcdir}/$file" && ! -f _) {
+	elsif (-l "$dir/$file" && ! -f _) {
 		error(sprintf(gettext("%s is not a file"), $file));
 	}
 	
@@ -46,7 +63,7 @@ sub check_canremove ($$$) {
 	# This is sorta overkill, but better safe than sorry.
 	if (! defined pagetype($pagesources{$page})) {
 		if (IkiWiki::Plugin::attachment->can("check_canattach")) {
-			IkiWiki::Plugin::attachment::check_canattach($session, $page, "$config{srcdir}/$file");
+			IkiWiki::Plugin::attachment::check_canattach($session, $page, "$dir/$file");
 		}
 		else {
 			error("removal of attachments is not allowed");
@@ -124,7 +141,7 @@ sub removal_confirm ($$@) {
 			my $f=IkiWiki::Plugin::attachment::is_held_attachment($page);
 			if (defined $f) {
 				require IkiWiki::Render;
-				IkiWiki::prune($f);
+				IkiWiki::prune($f, "$config{wikistatedir}/attachments");
 			}
 		}
 	}
@@ -223,21 +240,34 @@ sub sessioncgi ($$) {
 			require IkiWiki::Render;
 			if ($config{rcs}) {
 				IkiWiki::disable_commit_hook();
-				foreach my $file (@files) {
-					IkiWiki::rcs_remove($file);
+			}
+			my $rcs_removed = 1;
+
+			foreach my $file (@files) {
+				foreach my $srcdir (allowed_dirs()) {
+					if (-e "$srcdir/$file") {
+						if ($srcdir eq $config{srcdir} && $config{rcs}) {
+							IkiWiki::rcs_remove($file);
+							$rcs_removed = 1;
+						}
+						else {
+							IkiWiki::prune("$srcdir/$file", $srcdir);
+						}
+					}
+				}
+			}
+
+			if ($config{rcs}) {
+				if ($rcs_removed) {
+					IkiWiki::rcs_commit_staged(
+						message => gettext("removed"),
+						session => $session,
+					);
 				}
-				IkiWiki::rcs_commit_staged(
-					message => gettext("removed"),
-					session => $session,
-				);
 				IkiWiki::enable_commit_hook();
 				IkiWiki::rcs_update();
 			}
-			else {
-				foreach my $file (@files) {
-					IkiWiki::prune("$config{srcdir}/$file");
-				}
-			}
+
 			IkiWiki::refresh();
 			IkiWiki::saveindex();
 
diff --git a/IkiWiki/Plugin/transient.pm b/IkiWiki/Plugin/transient.pm
index 4ea4317d4..d4eb005ea 100644
--- a/IkiWiki/Plugin/transient.pm
+++ b/IkiWiki/Plugin/transient.pm
@@ -43,7 +43,7 @@ sub rendered (@) {
 		my $casualty = "$transientdir/$file";
 		if (srcfile($file) ne $casualty && -e $casualty) {
 			debug(sprintf(gettext("removing transient version of %s"), $file));
-			IkiWiki::prune($casualty);
+			IkiWiki::prune($casualty, $transientdir);
 		}
 	}
 }
diff --git a/IkiWiki/Render.pm b/IkiWiki/Render.pm
index d6c1f4f4c..a90d202ee 100644
--- a/IkiWiki/Render.pm
+++ b/IkiWiki/Render.pm
@@ -262,12 +262,13 @@ sub render ($$) {
 	}
 }
 
-sub prune ($) {
+sub prune ($;$) {
 	my $file=shift;
+	my $up_to=shift;
 
 	unlink($file);
 	my $dir=dirname($file);
-	while (rmdir($dir)) {
+	while ((! defined $up_to || $dir =~ m{^\Q$up_to\E\/}) && rmdir($dir)) {
 		$dir=dirname($dir);
 	}
 }
@@ -447,7 +448,7 @@ sub remove_del (@) {
 		}
 	
 		foreach my $old (@{$oldrenderedfiles{$page}}) {
-			prune($config{destdir}."/".$old);
+			prune($config{destdir}."/".$old, $config{destdir});
 		}
 
 		foreach my $source (keys %destsources) {
@@ -537,7 +538,7 @@ sub remove_unrendered () {
 		foreach my $file (@{$oldrenderedfiles{$page}}) {
 			if (! grep { $_ eq $file } @{$renderedfiles{$page}}) {
 				debug(sprintf(gettext("removing %s, no longer built by %s"), $file, $page));
-				prune($config{destdir}."/".$file);
+				prune($config{destdir}."/".$file, $config{destdir});
 			}
 		}
 	}
@@ -844,7 +845,7 @@ sub clean_rendered {
 	remove_unrendered();
 	foreach my $page (keys %oldrenderedfiles) {
 		foreach my $file (@{$oldrenderedfiles{$page}}) {
-			prune($config{destdir}."/".$file);
+			prune($config{destdir}."/".$file, $config{destdir});
 		}
 	}
 }
diff --git a/t/prune.t b/t/prune.t
new file mode 100755
index 000000000..8c3925e9e
--- /dev/null
+++ b/t/prune.t
@@ -0,0 +1,23 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+use Test::More tests => 6;
+use File::Path qw(make_path remove_tree);
+
+BEGIN { use_ok("IkiWiki"); }
+BEGIN { use_ok("IkiWiki::Render"); }
+
+%config=IkiWiki::defaultconfig();
+
+remove_tree("t/tmp");
+
+make_path("t/tmp/srcdir/a/b/c");
+make_path("t/tmp/srcdir/d/e/f");
+writefile("a/b/c/d.mdwn", "t/tmp/srcdir", "foo");
+writefile("d/e/f/g.mdwn", "t/tmp/srcdir", "foo");
+IkiWiki::prune("t/tmp/srcdir/d/e/f/g.mdwn");
+ok(-d "t/tmp/srcdir");
+ok(! -e "t/tmp/srcdir/d");
+IkiWiki::prune("t/tmp/srcdir/a/b/c/d.mdwn", "t/tmp/srcdir");
+ok(-d "t/tmp/srcdir");
+ok(! -e "t/tmp/srcdir/a");