relax SVN archive

New branch of the 1.3 line for the removal of apply(func, args) calls

See the relax-devel discussion at:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

This fixes a bug in the compile re function.

The bug was reported by Alex Hansen at https://mail.gna.org/public/relax-devel/2006-10/msg00112.html
(Message-id: <481156b20610190725ud6bab67w1f8fbbdf849da52c@...>). The simple fix is
described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html (Message-id:
<7f080ed10610190738g7df6566fl13b74d9217071924@...>).

Ported r2646 to r2647 from the 1.2 line.

The command used was:
$ svn merge -r2645:2647 svn+ssh://bugman@.../svn/relax/1.2

This adds a number of model-free optimisation tests to the test suite.

Ported r2643 from the 1.2 line.

The command used was:
$ svn merge -r2642:2643 svn+ssh://bugman@.../svn/relax/1.2

This includes a few small formatting changes to the model-free file.

Ported r2642 and r2644 of the 1.2 line (r2643 is not included).

The commands used were:
$ svn merge -r2641:2642 svn+ssh://bugman@.../svn/relax/1.2
$ svn merge -r2643:2644 svn+ssh://bugman@.../svn/relax/1.2

These changes include improvements to the infrastructure chapter of the relax user manual, and a
large expansion of the relax development chapter.

Ported r2641 from the 1.2 line.

The command used was:
$ svn merge -r2640:2641 svn+ssh://bugman@.../svn/relax/1.2

This fixes documentation bug #7402 (https://gna.org/bugs/?7402).

Ported r2637 to r2640 from the 1.2 line.

The command used was:
$ svn merge -r2636:2640 svn+ssh://bugman@.../svn/relax/1.2

This includes a number of changes to the Scons system including fixes for the distribution target
functions, the creation of the new module 'scons.install', and a restructure of the base
'sconstruct' file.

Ported r2635 from the 1.2 line.

The command used was:
$ svn merge -r2634:2635 svn+ssh://bugman@.../svn/relax/1.2

This involves a few functions moving to the new Scons module file 'scons/distrib.py'.

A fix for the function which loads the sequence from the PDB file.

This fixes two tests of the test suite. The changes already exist within the 1.3 line.

Speed ups for the optimisation tests in the test suite.

The grid search of each optimisation algorithm test has been replaced by the value setting function
as the results of the grid search are the same for each of the tests. As the grid search is
computationally expensive, this significantly speeds up the tests.