character encoding

When I run 'ls' on a given directory, some of the file names show a question mark in the place of a non-supported character. In trying to understand what is happening, I find that I don't understand a couple of fundamentals.

1. what is the default encoding of my debian system?
2. It seems that a file itself doesn't have any encoding as it is sitting on the hard drive -- its just bytes, right? when a given application picks it up, that application will try to read it as a certain encoding -- how is that determiniation made?
3. What is the encoding of the file name? Is this a feature of the filesystem?

I realize these questions may not be that "smart"; please tell me what I'm missing if so. Also, point me to documentation if you know of some that explains all of this. I couldn't find anything on the topic searching the web or debian docs.

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