The reason your header code is being ignored is because you are overwriting it. You open the file, write the header then close it, then later reopen the file using ">$file" which effectively erases it's contents, when you write the rest of you content. Use ">>$file" instead.

For the uninitialised error, I can only guess that you have lines in your input file that contain '#CCR-' that are not followed by anything. Hence you regex fails to capture anything into $functionName and your attempt to use it as a hash key in the line  $functxt{$functionName} = $desc;, results in the warning. An inspection of the input file, or testing for and warning of (and perhaps skipping), lines that do not result in a capture would be the surest way to test that hypothesis.