Почему при запуске системы вызывается команда rm

С GNU tar вы можете использовать -C когда угодно и когда угодно, с немедленным вступлением в силу .

$ tree
.
├── 1
│   └── aaa
├── 2
│   └── bbb
└── 3
    └── ccc



# Caveat: the directory change is always relative to directory tar is using *at
# that time*, so the following doesn't work:
$ tar -cf foo.tar -C 1 aaa -C 2 bbb -C 3 ccc  
tar: 2: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now

$ tar -cf foo.tar -C 1 aaa -C ../2 bbb -C ../3 ccc

$ tar tf foo.tar
aaa
bbb
ccc


# You can avoid the special case for the first directory by always specifying
# an absolute path:
$ tar -cf foo.tar -C $(pwd)/1 aaa -C $(pwd)/2 bbb -C $(pwd)/3 ccc



# Now let's create that automatically from your file:
$ cat mylist.txt
/tmp/1/aaa
/tmp/2/bbb
/tmp/3/ccc

$ while read -r line; do printf '-C %s %s ' $(dirname "$line") $(basename "$line") ; done < mylist.txt
-C /tmp/1 aaa -C /tmp/2 bbb -C /tmp/3 ccc 

# That looks about right. Let's use it in our tar command:
$ tar -cvf foo.tar $(while read -r line; do printf '-C %s %s ' $(dirname "$line") $(basename "$line") ; done < mylist.txt)
aaa
bbb
ccc