|It worked fine up to its planned limit of around 3000 files, but it's been too successful and the client now has 17,000 files in there!
A side note first: Some operating systems are really, really bad with directories that large. If your client is interested in performance, they (or you, on their behalf) may want to do a bit of performance prototyping. Recent work on FreeBSD has greatly improved its large directory performance, for whatever that's worth.
For your problem, I see two options: The first is to use File::Find to locate all *.txt files, and process them one-by-one. The second is to use opendir()/readdir()/closedir() to read the directory directly, filename by filename. Either one will avoid you having to hold on to a large temporary array.
You can find plenty of examples of each by using Super Search to look for "File::Find" or "opendir".
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