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It might help to know that in the German system, the notes are A - H, not A - G. In that system, what they call B is what we would call Bb (B flat). This system of 8 notes actually makes more sense in the harmonic series (the harmonic series is... umm... look it up? can't explain in one sentence), if you take your starting point as the note C instead of A. Take your guitar's open "G", which is the first partial of the harmonic series, there's a harmonic on the 12th fret, which is a G an octave higher - that's the 2nd partial. At the 7th fret is a D (the third partial), another G at the 5th fret, a B at the 4th (4th partial), another D... and so on. Well, if this string was an ideal/theoretical string, you would soon run into a series of partials that would be a G major scale, except that it would also have an F natural. Transpose that to C, and you have some understanding of the German system. It is quasi-scientifically based. If you keep going up the harmonic series, it eventually becomes completely chromatic.
Now, that only really works for the musical system that's been in place for the last few hundred years: harmonic tonality. Ancient Greek and Islamic music theory relied on the harmonic series, but moving the focus to very different areas which I won't get into here. What's funny is that in the Renaissance, there was a real interest in Greek music theory, without much understanding of it, though some of the terms were borrowed, words used to describe the different modes, for instance.
Now, before tonal music came into being, western music was modal. That is, instead of relying on moving from one chord to another, it was all based on melody, like in monastic chanting (some of these chants date back to the middle ages). In a modal system, there was no changing of keys. You know, in a piece now, you can move from the key of C to the key of G. In both of those keys - any key - in a piece of music, they are related to their respective root note, with this same harmonic series that I described as taking place via harmonics on the guitar. See, in medieval music, there wasn't this movement of keys. Different pieces could start on different notes, but there was always a fixed relationship between these notes within a piece - there would never be more than 7 different notes in a piece, so they didn't need to have names for more than 7 notes (maybe I should I have said this at the beginning?). This part I'm not completely sure of, but I think my conjecture is right - what we call the Aeolian mode (then and now) was the most common. It's also now called "natural minor". If you start that mode on A, you have A, B, C, D, E, F, G - since they wouldn't have more notes than that in a piece of music, they're just named in the order they come in that mode. All of the monastic modes also only include this notes, or these note relationships, transposed. For instance, the Dorian mode is just D - C, with the 1/2 steps between B/C and E/F. Once different/more complicated music came into being, a lot of the old terminology was just carried over.
I'm sure that I could have explained this much more clearly if I wasn't just writing off the cuff, but that's why I'm not a music theory or music history expert (I am a composer though - like, a real one - no, one here would have heard my stuff, unless you're one of the few dozen who go to tiny experimental music concerts and festivals).
It doesn't deal with this stuff exactly, but a book that I would very highly recommend is called "A History of Consonance and Dissonance", by James Tenney. There are loads of music theory text books out there, but this one is the only book that I know that explains how thoughts about music making, and the terminology that goes with it, changed from the medieval period to the 20th century.
If you need me to clarify something or have another question, just ask. Good luck with the guitar playing!
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