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Why can Windows command prompt run this file?

I have a ./configure file that I'm supposed to run by putting it in the command prompt. It works when I run it in the git prompt but when I run it in the Windows command prompt it gives me:

C:\cygwin\home\doxygen\configure> configure
'configure' is not recognized as an internal or external command,
operable program or batch file.

Even though I'm in the correct directory (and running dir shows me that the file is there) it still stays that it cannot find the file. This is the same for all files that don't have an extension on them. Why does this happen and how can I get this to work?

./configure is not a program. It's more of a shell script usually. My analogy may not be good but consider it to be the equivalent of windows batch files (in this case you can say it's a .sh without the extension). It will only run from a cygwin/unix shell.

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