bugfix: cleanup nested auto generated variant directories

src/tup/create_name_file.c

@@ -632,6 +632,15 @@ tupid_t find_dir_tupid_dt_pg(tupid_t dt, struct pel_group *pg,
 						fprintf(stderr, "' is a %s\n", tup_db_type(tent->type));
 						return -1;
 					}
+				} else if(sotgv == SOTGV_IGNORE_DIRS && !(pg->pg_flags & PG_OUTSIDE_TUP) &&
+					  tent->type == TUP_NODE_GHOST) {
+					/* Ignored files inside the project are normal files,
+					 * so their ancestors must be normal directories even
+					 * when a previous missing-path read created ghosts.
+					 */
+					if(tup_db_set_type(tent, TUP_NODE_DIR) < 0)
+						return -1;
+					tup_db_del_ghost_tree(tent);
 				}
 			} else {
 				int type = TUP_NODE_GHOST;

src/tup/db.c

@@ -1732,7 +1732,7 @@ static int delete_variant_dir(struct tup_entry *tent, void *arg, int (*callback)
 		if(tup_entry_add(he->tupid, &subtent) < 0)
 			return -1;
 
-		if(he->type == TUP_NODE_DIR) {
+		if(he->type == TUP_NODE_DIR || he->type == TUP_NODE_GENERATED_DIR) {
 			flags = AT_REMOVEDIR;
 			if(delete_variant_dir(subtent, arg, callback) < 0)
 				return -1;

test/t5123-ignore-output-ghost-dir.sh

@@ -0,0 +1,55 @@
+#! /bin/sh -e
+# tup - A file-based build system
+#
+# Copyright (C) 2026  Mike Shal <marfey@gmail.com>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License version 2 as
+# published by the Free Software Foundation.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+# An excluded write must convert existing ghost ancestors to normal directories,
+# just as it does when those directory entries do not already exist.
+. ./tup.sh
+
+cat > Tupfile << HERE
+: |> sh run.sh |> stamp ^/temp_files/temporary.txt
+HERE
+cat > run.sh << HERE
+cat temp_files/test 2>/dev/null || echo missing
+touch stamp
+HERE
+update
+tup_object_exist . temp_files
+
+cat > Tupfile << 'HERE'
+: |> sh run.sh |> stamp ^/temp_files(/(?!.*test$).*)?$
+HERE
+cat > run.sh << HERE
+mkdir -p temp_files/nested
+echo ignored > temp_files/temporary.txt
+echo ignored > temp_files/nested/temporary.txt
+touch stamp
+HERE
+update
+check_exist temp_files/temporary.txt
+check_exist temp_files/nested/temporary.txt
+
+# The next scan used to load the normal file without its ghost parent and fail
+# with "Unable to find parent entry". Check repeated scans and deletion too.
+tup scan
+update
+rm -rf temp_files
+tup scan
+update
+tup_object_no_exist . temp_files
+
+eotup

test/t5124-ignore-output-ghost-dir-signalled.sh

@@ -0,0 +1,56 @@
+#! /bin/sh -e
+# tup - A file-based build system
+#
+# Copyright (C) 2026  Mike Shal <marfey@gmail.com>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License version 2 as
+# published by the Free Software Foundation.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+# Interrupted commands also process excluded writes. They must not leave normal
+# files beneath ghost directories and prevent the next scan from running.
+. ./tup.sh
+check_no_windows process
+
+cat > Tupfile << HERE
+: |> exec sh run.sh |> stamp ^/temp_files/temporary.txt
+HERE
+cat > run.sh << HERE
+cat temp_files/test 2>/dev/null || echo missing
+touch stamp
+HERE
+update
+tup_object_exist . temp_files
+
+cat > Tupfile << 'HERE'
+: |> exec sh run.sh |> stamp ^/temp_files(/(?!test$).*)?$
+HERE
+cat > run.sh << 'HERE'
+mkdir -p temp_files
+echo ignored > temp_files/temporary.txt
+kill -TERM $$
+HERE
+update_fail_msg 'killed by signal 15'
+tup scan
+
+# The interrupted command must remain pending, and a subsequent successful
+# update must be able to complete without rebuilding the database.
+cat > run.sh << HERE
+mkdir -p temp_files
+echo ignored > temp_files/temporary.txt
+touch stamp
+HERE
+update
+tup scan
+update
+
+eotup

test/t8120-variant-remove-generated-dirs.sh

@@ -0,0 +1,44 @@
+#! /bin/sh -e
+# tup - A file-based build system
+#
+# Copyright (C) 2026  Mike Shal <marfey@gmail.com>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License version 2 as
+# published by the Free Software Foundation.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+# Regression for 698ff025: removing a variant must recursively clean generated
+# directories, not just directories copied from the source tree.
+. ./tup.sh
+
+mkdir build
+echo CONFIG_BUILD=y > build/tup.config
+cat > Tupfile << HERE
+ifeq (@(BUILD),y)
+: |> echo generated > %o |> generated/nested/output.txt
+endif
+HERE
+update
+check_exist build/generated/nested/output.txt
+tup_object_exist build/generated nested
+tup_object_exist build/generated/nested output.txt
+
+# Leave the physical directories in place so delete_variant_dir() has to recurse
+# into them. Removing the entire variant beforehand would miss this regression.
+rm build/tup.config
+update
+check_not_exist build/generated
+tup_object_no_exist build generated
+tup scan
+update
+
+eotup