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I have a lot of domains and it's getting hard to manage so I want to add a string to the end of every file opened in Apache so I can request any domain if check if the string is there so I will know the domain is working and with my dns.

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Mod_Layout should do the trick; it allows you to add a header/footer to all displayed pages of a certain file type, so you could add your string as a HTML comment.

<!-- This webpage is provided by XCompany! -->

And search for that. Shouldn't effect any of the websites while giving you what you need.

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