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Changing the executable after loading (e.g. Ninite)

I am currently developing an application (Windows) that requires internal changes at boot time. In addition, I deliver it using the Linux host, so it cannot compile on demand, as suggested.
How does it work Ninite ?
At Ninite.com, every time you select different options, you get the same .exe, however, with minor changes inside.

Option 1
Compile a program with predefined data (on Windows).
Use PHP to view the file and replace your own lines.

Option 2
Add the original .EXE with another resource file

Other

Has anyone developed this? What would be a better approach?
Thank.

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2 answers

You can simply add data back to the original executable. The Windows PE file format is simple enough that it does not invalidate the executable itself. (However, this will invalidate any existing digital signatures.)

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