relax SVN archive

Large simplification of the atomic coordinate assembly code in the internal structural object.

This is in the lib.structure.internal.coordinates.assemble_coord_array() function. The logic of the
function has recently changed due to the introduction of the pairwise sequence alignments. This
caused a lot of code to now be redundant, and also incorrect in certain cases. This simplification
fixes the problem caught by the Structure.test_align_molecules2 system test.

Created the Structure.test_align_molecules2 system test.

This is to demonstrate a failure condition in the structure.align user function.

Spelling fixes for the CHANGES document.

Updated the relax version number to 3.3.5 on the http://www.nmr-relax.com/api/index.html webpage.

Updated the relax API documentation at http://www.nmr-relax.com/api/3.3/ to version 3.3.5.

Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to version 3.3.5.

Updated the http://www.nmr-relax.com/download.html webpage for relax 3.3.5.

Backported the relax 3.3.5 CHANGES file changes to trunk.

The command used was:
svn merge -r27329:27330 svn+ssh://bugman@.../svn/relax/tags/3.3.5 .

Updated the CHANGES file for relax 3.3.5.

Introduced the nested_params_ave_dom_pos argument to the frame order auto-analysis.

This allows the average domain position to be set to no rotations and translations rather than
taking the average position from the rotor or free-rotor model. This can be useful when large
motions are present causing the rigid model to have unreasonable domain positions.