Moved examples out of main repo (now in MDAnalysisCookbook)

Closes Issue #627

package/MANIFEST.in

@@ -8,7 +8,6 @@ include MDAnalysis/lib/src/transformations/*
 recursive-include doc * 
 include README INSTALL CHANGELOG LICENSE AUTHORS SUMMARY.txt
 include setup.py
-recursive-include examples *
 global-exclude *.pyc
 global-exclude *.pyo
 global-exclude *.pyd

package/MDAnalysis/analysis/gnm.py

@@ -29,8 +29,12 @@
 
 Analyse a trajectory using elastic network models, following the approach of [Hall2007]_.
 
-An example is provided in :file:`examples/GNMExample.py`. The basic
-approach is to pass a trajectory to :class:`GNMAnalysis` and then run
+An example is provided in the MDAnalysis Cookbook_, listed as GNMExample_.
+
+.. GNMExample_: https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/GNMExample.py
+.. Cookbook_: https://github.com/MDAnalysis/MDAnalysisCookbook
+
+The basic approach is to pass a trajectory to :class:`GNMAnalysis` and then run
 the analysis::
 
    u = MDAnalysis.Universe(PSF,DCD)

package/MDAnalysis/analysis/leaflet.py

@@ -38,11 +38,13 @@
   of distances from the centre of geometry (or possibly simply the
   :meth:`~MDAnalysis.core.AtomGroup.AtomGroup.radius_of_gyration`).
 
-See example scripts in the ``examples/`` directory on how to use
+See example scripts in the MDAnalysisCookbook_ on how to use
 :class:`LeafletFinder`. The function :func:`optimize_cutoff` implements a
 (slow) heuristic method to find the best cut off for the LeafletFinder
 algorithm.
 
+.. MDAnalysisCookbook_: https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples
+
 .. autoclass:: LeafletFinder
    :members:
 

package/doc/sphinx/source/documentation_pages/overview.rst

@@ -198,23 +198,23 @@ and more.
 .. Links to the stable git repository:
 
 .. _examples:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/
+   https://github.com/MDAnalysis/MDAnalysisCookbook/tree/master/examples/
 
 .. _`rmsfit_qcp.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/rmsfit_qcp.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/rmsfit_qcp.py
 .. _`blocks.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/blocks.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/blocks.py
 .. _`potential_profile.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/potential_profile.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/potential_profile.py
 .. _`nativecontacts.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/nativecontacts.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/nativecontacts.py
 .. _`membrane-leaflets.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/membrane-leaflets.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/membrane-leaflets.py
 .. _`multimers-analysis.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/multimers-analysis.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/multimers-analysis.py
 .. _`dcd2xtc.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/dcd2xtc.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/dcd2xtc.py
 .. _`amber2dcd.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/amber2dcd.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/amber2dcd.py
 .. _`make_MthK_tetramer.py`:
-   https://github.com/MDAnalysis/mdanalysis/blob/master/package/examples/make_MthK_tetramer.py
+   https://github.com/MDAnalysis/MDAnalysisCookbook/blob/master/examples/make_MthK_tetramer.py