relax SVN archive

Added redirects for all renamed user functions for the HTML version of the manual.

Set up a new redirect for the frq.set to spectrometer.frequency user function name change.

This is for the HTML manual.

Renamed the pseudo-ellipse permutation directory to perm_pseudo_ellipse_x_le_y_le_z.

This is for the CaM frame order rotor model synthetic data.

Updated the frame order pseudo-ellipse motion permutation test data.

This is for the CaM frame order rotor model synthetic data. The correct axis and cone angle
permutations of the frame_order.permute_axes user function are now being used and optimised.

Redesign of the axis permutation algorithm of the frame_order.permute_axes user function.

Instead of tracking the fact that cone_theta_x is a rotation around the y-axis and cone_theta_y is
about the x-axis, now two permutation arrays are created - one for the three angles and one for the
axes. The permutation array values have also been completely changed as previously the incorrect
inverse permutation was coded into the algorithm.

Bug fix for the new frame_order.permute_axes user function.

The cone and torsion angles were not being correctly permuted. Now the direct permutation array is
being used. And the fact that cone_theta_x is a rotation along the y-axis and cone_theta_y along
the x-axis is taken into account.

Created some test data files for visualising the frame order axis permutation.

This uses the CaM frame order synthetic data for the rotor model to visualise the pseudo-ellipse
frame order model axis permutations. The initial conversion sets the pseudo-ellipse torsion angle
cone_sigma_max to the rotor opening half-angle, and the pseudo-elliptic cone opening to close to
zero. Then the axis permutations are performed. All three solutions are optimised. PDB
representations before and after optimisation are included to illustrate any problems.

Fix for the axis permutation protocol in the frame order auto-analysis.

The pipe.copy user function does not switch pipes, therefore the pipe.switch user function is now
being called so that the correct pipe is being permuted and optimised.

Many fixes for the frame_order.permute_axes user function.

The z-axis inversion is now encoded into a 3D numpy array as the index of the new z-axis position
needs to be stored. The cone_theta_x, cone_theta_y and cone_sigma_max parameters are now permuted
in reverse 'perm' data structure by calling its index() method. And the cone_theta_x - cone_theta_y
to y-axis - x-axis switch has been removed (this may need to be reintroduced later).

Fix for the Frame_order.test_axis_perm_x_le_z_le_y_permB system test.

The permuted z-axis needs to be inverted in the test.