Deprecate and simplify nut modules in utilities

There are a few unused or underused generalised nut modules in utilities.scad.

• nut() - unused
• nut_from_bottom() - unused
• nut_y() - used exactly ones

All 3 of them have a nominal d input, and then use a somewhat arbitrary calculation with fudge factors to get the correct size. However, as metric nut sizes do not scale linearly with their nominal diameter, the function is not universal as is implied.

It might be possible to link them to a lookup table, but I think that the only values we are confident on based on extensive testing are M3.

Suggestion

• Remove nut() and nut_from_bottom() (or if not link them to m3 as below)
• Replace nut_y() with m3_nut_y(). Removing the arbitrary calculation and just used fixed numbers that have now been tested by long term use. If we want some calculation we should probably use the ISO specified dimensions across flats. Calculate the corner widths from there, then add a clearance. This will make it significantly more clear.