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It's a Windows shell (cmd) command. If you need it in a batch file, you need to escape the %. Change %q to %%q.
Cygwin is a OS emulator, not a shell or a scripting language. When people say Cygwin, they usually refer to bash and/or GNU tools. samtregar showed that a solution can be obtained using bash and GNU tools. I showed that such tools weren't required.
It invokes perl. -p and -i are documented in perlrun. In reply to Re^4: Automatically Rewrite Shebang Line on Multiple Files
by ikegami
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