Three points, after a quick scan through your code:
Using $^O =~ /win/ to detect Windows systems will fail to detect 'MSWin32' as a Windows system, and will falsely detect 'Darwin'. This was an issue for the CGI module on p5p recently; the recommended solution was $^O =~ /^MSWin/i.
Removing a trailing slash from a path can be done more easily with a regex than with substr:
$cwd = getcwd();
$path = $ENV{'DOCUMENT_ROOT'};
if ($^O =~ /^MSWin/i) {
$cwd =~ s,\\$,,;
$path =~ s,\\$,,;
} else {
$cwd =~ s,/$,,;
$path =~ s,/$,,;
}
However, / can be used as a directory separator in Perl on Windows, and there are other operating systems, besides Unix and Windows, and they don't all use slash or backslash as the directory separator. File::Spec would be a portable way of dealing with this issue.
Finally... Have you tested your code with HTML that contains multiple SSI directives on the same line?
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