Avoid Matrix::diagonal and limit progress bar updates

[matt-graham]

From some profiling

• Matrix-vector multiplications using %*% with Matrix::Diagonal appear to be much slower than just using a diagonal matrix constructed with diag even though nominally this incurs an unecessary quadratic rather than linear cost.
• Progress bar updates become bottleneck when chain iterations are very fast.

This PR therefore switches to using diag in place of Matrix::Diagonal and limiting progress bar updates to every 10% (or every 1 iteration if less than 10 iterations).

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (5d29b85) to head (1d3fe26).
Report is 18 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main       #47   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files           11        11           
  Lines          480       483    +3     
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+ Hits           480       483    +3     

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