Я получил этот скрипт, который читает часть моего файла с разделителями .gitignore и удаляет все файлы после данной метки # #:

# https://stackoverflow.com/questions/55527923/how-to-stop-makefile-from-expanding-my-shell-output
RAW_GITIGNORE_CONTENTS := $(shell while read -r line; do printf "$$line "; done < ".gitignore")
GITIGNORE_CONTENTS := $(shell echo "$(RAW_GITIGNORE_CONTENTS)" | sed -E $$'s/[^\#]+\# //g')

# https://stackoverflow.com/questions/4210042/exclude-directory-from-find-command
DIRECTORIES_TO_CLEAN := $(shell /bin/find -not -path "./**.git**" -not -path "./pictures**" -type d)

clean:
#   https://stackoverflow.com/questions/10586153/split-string-into-an-array-in-bash
#   https://stackoverflow.com/questions/11289551/argument-list-too-long-error-for-rm-cp-mv-commands
    readarray -td' ' GARBAGE_DIRECTORIES <<<"$(DIRECTORIES_TO_CLEAN) "; \
    unset 'GARBAGE_DIRECTORIES[-1]'; \
    declare -p GARBAGE_DIRECTORIES; \
    readarray -td' ' GARBAGE_EXTENSIONS <<<"$(GITIGNORE_CONTENTS) "; \
    unset 'GARBAGE_EXTENSIONS[-1]'; \
    declare -p GARBAGE_EXTENSIONS; \
    for filename in "$${GARBAGE_DIRECTORIES[@]}"; \
    do \
        arraylength = "$${#GARBAGE_EXTENSIONS[@]}"; \
        printf 'Cleaning %s extensions on %s\n' "$${arraylength}" "$$filename"; \
        for extension in "$${GARBAGE_EXTENSIONS[@]}"; \
        do \
            [[ ! -z "$$filename" ]] || continue; \
            [[ ! -z "$$extension" ]] || continue; \
            full_expression = "$${filename}/$${extension}" ;\
            printf '%s\n' "$$full_expression"; \
            rm -v "$$full_expression"; \
        done; \
    done;

Запускаем его со следующим .gitignore файлом:

*.txt
*.var
# Comment #
*.aux

Команда rm не расширяет подстановочные знаки и продолжает говорить мне rm: cannot remove './*.aux': No such file or directory и не удалять файлы *.aux из каталога ./.

Обновлять

После вопроса о комментарии @Beta я упростил Makefile до этого:

GITIGNORE_CONTENTS := "*.aux" "*.lof"
DIRECTORIES_TO_CLEAN := "./setup/cache" "./setup/cache/chapters"

clean:
    readarray -td' ' GARBAGE_DIRECTORIES <<<"$(DIRECTORIES_TO_CLEAN) "; \
    unset 'GARBAGE_DIRECTORIES[-1]'; \
    declare -p GARBAGE_DIRECTORIES; \
    readarray -td' ' GARBAGE_EXTENSIONS <<<"$(GITIGNORE_CONTENTS) "; \
    unset 'GARBAGE_EXTENSIONS[-1]'; \
    declare -p GARBAGE_EXTENSIONS; \
    for filename in "$${GARBAGE_DIRECTORIES[@]}"; \
    do \
        arraylength = "$${#GARBAGE_EXTENSIONS[@]}"; \
        printf 'Cleaning %s extensions on %s\n' "$${arraylength}" "$$filename"; \
        for extension in "$${GARBAGE_EXTENSIONS[@]}"; \
        do \
            [[ ! -z "$$filename" ]] || continue; \
            [[ ! -z "$$extension" ]] || continue; \
            full_expression = "$${filename}/$${extension}" ;\
            printf '%s\n' "$$full_expression"; \
            rm -vf "$$full_expression"; \
        done; \
    done;

Какие результаты на этом выходе после его запуска:

$ make
readarray -td' ' GARBAGE_DIRECTORIES <<<""./setup/cache" "./setup/cache/chapters" "; \
unset 'GARBAGE_DIRECTORIES[-1]'; \
declare -p GARBAGE_DIRECTORIES; \
readarray -td' ' GARBAGE_EXTENSIONS <<<""*.aux" "*.lof" "; \
unset 'GARBAGE_EXTENSIONS[-1]'; \
declare -p GARBAGE_EXTENSIONS; \
for filename in "${GARBAGE_DIRECTORIES[@]}"; \
do \
        arraylength = "${#GARBAGE_EXTENSIONS[@]}"; \
        printf 'Cleaning %s extensions on %s\n' "${arraylength}" "$filename"; \
        for extension in "${GARBAGE_EXTENSIONS[@]}"; \
        do \
                [[ ! -z "$filename" ]] || continue; \
                [[ ! -z "$extension" ]] || continue; \
                full_expression = "${filename}/${extension}" ;\
                printf '%s\n' "$full_expression"; \
                rm -vf "$full_expression"; \
        done; \
done;
declare -a GARBAGE_DIRECTORIES=([0] = "./setup/cache" [1] = "./setup/cache/chapters")
declare -a GARBAGE_EXTENSIONS=([0] = "*.aux" [1] = "*.lof")
Cleaning 2 extensions on ./setup/cache
./setup/cache/*.aux
./setup/cache/*.lof
Cleaning 2 extensions on ./setup/cache/chapters
./setup/cache/chapters/*.aux
./setup/cache/chapters/*.lof

Больше упрощения

Я сократил до более простой версии, которая может быть:

clean:
    rm -v "./setup/cache/*.aux";

Запустив это, также не удаляйте файлы:

$ make
rm -v "./setup/cache/*.aux";
rm: cannot remove './setup/cache/*.aux': No such file or directory
make: *** [Makefile:3: clean] Error 1

$ ls ./setup/cache/*.aux
./setup/cache/main.aux

Выше, после запуска ls, вы можете видеть, что файл все еще существует, и он там.