Delete all files in a directory whose name do not match a line in a file list

Pre-construct the arguments to find:

{
  read -r
  keep=( -name "$REPLY" ) # no `-o` before the first one.
  while read -r; do
    keep+=( -o -name "$REPLY" )
  done
} < file_list.txt
find . -type f ! \( "${keep[@]}" \) -exec echo rm {} +

Use the echo parts to see what would be constructed. Remove the echo parts to actually run it.

Update: Demonstration:

##
# Demonstrate what files exist for testing.
# Show their whitespace:
~/foo $ printf '"%s"\n' *
" op"
" qr"
"abc"
"def"
"gh "
"ij "
"k l"
"keep"
"m n"

##
# Show the contents of the "keep" file,
# Including its whitespace:
~/foo $ cat -e keep
keep$
abc$
gh $
k l$
 op$

##
# Execute the script:
~/foo $ { read -r; keep=( -name "$REPLY" ); while read -r ; do keep+=( -o -name "$REPLY" ); done } < keep
~/foo $ find . -type f ! \( "${keep[@]}" \) -exec rm {} +

##
# Show what files remain:
~/foo $ printf '"%s"\n' *
" op"
"abc"
"gh "
"k l"
"keep"

With zsh:

mylist=(${(f)"$(<filelist)"})
print -rl -- *(.^e_'(($mylist[(Ie)$REPLY]))'_)

It reads the lines of filelist in an array and then uses glob qualifiers/estring to glob/select only the file names not present in the array: the . selects only regular files (add D if your list contains dotfiles) and the negated ^e_'expression'_ further selects only those for which the expression returns false, i.e. if their name ($REPLY) is not an element of the array.
If you're happy with the result replace print -rl with rm to actually remove the files:

rm -- *(.^e_'(($mylist[(Ie)$REPLY]))'_)

To select & remove files recursively, use the */** glob with ${REPLY:t} glob modifier:

rm -- */**(.^e_'(($mylist[(Ie)${REPLY:t}]))'_)

If you put the contents of the directory into a file like so:

cd <somedirectory>
ls >> filelist

Open filelist with a text editor, and remove all the files except the ones YOU WANT TO DELETE. That's bolded because it's the opposite approach to the answer above

Try this:

while read p || [[ -n $p ]]; 
echo $p
done < filelist

If you see your list of files output to the screen replace echo with rm -v, like so:

while read p || [[ -n $p ]]; 
rm -v $p
done < filelist

Run the below script.

1. Initially I am finding all the files that are present inside the directory and storing the output to another file all_files.
2. We have a file which has the list of files that should NOT be deleted (not_to_be_deleted_files).
3. I am adding the file names not_to_be_deleted_files and files_to_be_deleted to the end of not_to_be_deleted_files as we need these 2 files.
4. Now, I am finding the files that needs to be deleted using linux join command and redirecting the output to files_to_be_deleted file.
5. Now, in the final while loop I am reading all the file names in files_to_be_deleted and removing the files mentioned in that file name.

The script is as below.

find /home/username/directory -type f | sed 's/.*\///' > all_files
echo all_files >> not_to_be_deleted_files
echo not_to_be_deleted_files >> not_to_be_deleted_files
echo files_to_be_deleted >> not_to_be_deleted_files
join -v 1 <(sort all_files_listed) <(sort files_not_to_be_deleted) >   files_to_be_deleted
while read file
rm  "$file"
done < files_to_be_deleted

P.S: Probably, if you wish this to be saved as a script and run it, you can add the script name also using echo scriptname >> not_to_be_deleted_files.

Though it is not required, I prefer to do it because there will be no regrets later. I tested for a small set of files and it worked in my system. However, if you want to be sure, try in a test directory first and then remove the files in the original directory.

• Use the list as a source, to move all files in the list to a fresh, new and empty save-dir.
• Compare the number of files in the list and the number of saved files.
• If both match, delete all unsaved files with your favorite method.
• Move the saved files back.

I went for a safer and much, much faster approach because I had 18.000 files in the list! I needed to clean up images in a large Drupal installation.

Deleting all the files that are not in the list is the same as keeping only those that are in the list. So I decided to actually copy the files from the list to another location, but copying 20 GB of files would take up too much space and be very slow as well. So the trick is to copy the files as hardlinks instead, using the -l option of cp. This takes up almost no space and is very fast. Additionally, since I needed to preserve the directory structure, I used the --parents option.

Here is an excerpt from my file list:

1px.png
misc/feed.png
modules/file/icons/x-office-presentation.png
modules/file/icons/x-office-spreadsheet.png
newsletter.png
sites/all/libraries/ckeditor/plugins/smiley/images/devil_smile.png
sites/all/libraries/ckeditor/plugins/smiley/images/regular_smile.png
sites/default/files/009313_PwC_banner_CBS_Observer_180x246px.jpg

So an example line would be, with temp being the destination:

cp -l --parents 'misc/feed.png' temp

This will create this structure:

temp
  misc
    feed.png

Note that the destinaton must be in the same file system as the source for hardlinks to work.

The next step is to construct the script:

sed -e "s,^,cp -l --parents '," -e "s,$,' /some/where/temp," filelist > newfilelist

Now, presuming you already created the empty dir /some/where/temp, you can copy the files like this:

sh newfilelist 2> missing_files

Note how errors end up in missing_files. The added bonus of this approach is that you will get a list of files from the original list that actually don't exist!

After running the script, temp will contain only those files that are in the file list, but without deleting anything and without taking up additional space. If you are satisfied with the result, you can delete all the orginal files including the subfolders.

Finally, move the files and folders from temp back to the original location.

For the 18.000 files it took only a few seconds.

Safe, simple.

cd to directory.

Create a temp directory.

mv *.yourExlusionSelector.* ./temp
rm *
mv ./temp ./
rm -rf ./temp

done.