My own stuff in Applications?

I've recently converted from PC to Apple, and I'd like to ask a fundamental question: can I put my own stuff, like docs, in the Applications folder?
I've been in the habit of making some kind of crib sheet for rarely-used programs (and those whose interface isn't totally intuitive). So suppose I install a third party program called Boggis: I might create Boggis.txt or similar. Am I allowed to put that in Applications?
The reason I ask is that I sometimes find some doc of this type has mysteriously vanished. So does some process like Software Update police the Applications folder? Or could it be that when I install an updated Boggis, it deletes all files starting "Boggis" in Applications?
I'm aware that "Applications" is actually more than just one folder. And if it matters, I'm the primary user so there's no problem with permissions.
So what's the answer please?
  Mac OS X (10.4.9)  

You can stick whatever you want in the Applications folder, but that's not the right place for something like that, /Users/Shared is.
There's no process that clears out/moves stuff in the apps folder. There is a software update process that will update apps if they are in their expected locations within that folder, and there's a script that will change the permissions on files in that folder, but that's about it.
However, most people expect to find applications in /Applications. That's what it's there for. If you have a crib-sheet for your own personal use, then ~/Documents or ~/Desktop would be approriate places. If its general documentation for everyone to use/access, then /Users/Shared is the most logical place to look.
Keep in mind that Spotlight is going to index your document too. You can go to the little magnifying glass icon in the right-most location of your menu bar and click on it and type the name of your document, or some of the text you know lies inside and it'll find it for you wherever you put it. However, if there are other users on your Mac they won't be able to see the file if it's in your account (unless it is in your ~/Public folder).

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