I think you want to test with "$file eq "@onefile" whether $file is contained in the array @onefile.

This is the wrong syntax.

What I would do is using a hash:

my %onefile= map { $_ => 1 } readdir(TMP);
# Now every file in TMP is a key in the hash
...
# and later we check like this:
foreach $file (@allfiles)
{
 if ($onefile{$file})
...
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