Linux – Create new empty directory tree from existing tree with files

You can put some more glob pattern in front of ../foo like this:

cp -R -s ../foo/* .

This will create relative symbolic links in current directory of all files/directories found in ../foo/* path.

If you want to copy only those files whose names are listed in filelist.txt, and skip files that aren't (e.g., file3.jpg in your example), do

for /r folder %f in (*) do @findstr/i /x "%~nxf" filelist.txt > nul && copy %f secondfolder

• %f is assigned the full pathname of each file under folder; %~nxf extracts the name and extension (i.e., the base filename; everything after the last \).
• @ suppresses display of the following command.  This is cosmetic and discretionary.  Also, it is unnecessary if you put this command in a batch file and begin it with @echo off.
• findstr looks for a string (or pattern) in a file (or other data set); it is essentially Windows' equivalent of grep.  We use it to determine whether each filename is in the filename list, filelist.txt.
  • /i — Do case insensitive matching.  You can leave this out if you're sure your list has correct capitalization.
  • /x — Match entire line (like grep -x).  This prevents filenames like le2.do from matching file2.doc.
• > nul — equivalent to > /dev/null; this prevents the output from findstr from being displayed.  (Of course this is just to avoid cluttering the screen, and is optional.)
• && — Do the next command (copy) if the previous command (findstr) succeeded.  (findstr succeeds if it finds a match; i.e., if the filename is in the list.)
• If you have any filenames with funny characters in them, you may need to put the last %f into quotes ("%f") and maybe change the findstr command.
• Before you run this command for real, you might want to change copy to echo copy, so you can do a dry run and see what the command will do.
• If you put the command into a batch file, change all occurrences of % to %%.
• If you want to get a listing (log) of where the files were found, you can do

for /r folder %f in (*) do @findstr/i /x "%~nxf" filelist.txt > nul && (echo %f & copy %f secondfolder)