Little-known fact: the "-i" flag just sets the $^I variable. You can set it yourself. Then setting @ARGV, reading <>, and printing the result is all you have to do. Thus:

local $^I = '.bak';
local @ARGV = ("$dir/$header_file");
while (<>) {
    s/foo/bar/;  # whatever you want
    print;
}
[download]

Presto, magico, all done!

    -- Chip Salzenberg, Free-Floating Agent of Chaos