migration guide for 0.10 to 0.11 transition

[orbeckst]

With the big API changes in the 0.11.0 release, we need documentation to support the users in transitioning their existing code. @tylerjereddy already started the wiki page MDAnalysis 0.11 unifying release user guide.

This page (and possibly others, as needed, such as the Releases Notes for 0.11.0) have to be up-to-date and complete before the release so that we can send users to those pages.

[tylerjereddy]

MDAnalysis 0.11 user guide sections that require developer verification (please edit and fill in as below if you are comfortable verifying an example covering a particular API change):

API Change	Verified by a Developer ?
Removed Contact Matrix progress meter
New Timestep behaviour	Richard
atomgroup methods to properties and select_atoms replacing selectAtoms	Tyler
Atom.number renamed to Atom.index	Tyler (but Atom.number still works in my hands)
Migration of some code to MDAnalysis.lib	Tyler (but could use some more examples; also, these are deprecations rather than hard replacements?)
Timestep._x _y and _z are now read only	Richard
numberOfAtoms() to n_atoms and others	Tyler
Renamed topology methods	Richard
Frame numbering is now 0-based	Tyler

[mnmelo]

The global selection keyword, proposed in #268, deprecates the fullgroup one, and I thought it'd be good to bundle this change together with the 0.11 breaking changes.

I just submitted PR #394 with the update, and will add a section on the migration guide.

[orbeckst]

Note on deprecations: anything that was deprecated should be changed. A user who has applied all changes in the guide should not see any deprecation warnings any more.