Fix IPython.start_kernel()

Closes gh-4005
Fix passing user_ns to IPython.start_ipython()
Fix passing user_ns to IPython.start_kernel()
Use traitlet on InteractiveShellApp instead of storing user_ns via __init__
Add REPL-like printing to %%R cell magic
Fix warning when running IPython.kernel tests

The signature of TemporaryDirectory.cleanup() changed just before Python 3.2, and our
TemporaryWorkingDirectory subclass was receiving an unexpected parameter. This copies
in a newer TemporaryDirectory.cleanup() implementation for Python 2.7.
made docstrings clearer and more explicit/correct for eval and R methods
Use print_function in IPython.utils.tempdir
moved printing logic to the R magic function (out of the eval function)
removed unnecessary parentheses
Fix parallel.client.View map() on numpy arrays
Fix test_map_iterable()
DOC: fix links to matplotlib, notebook docs

I've added a link to pandas, made all matplotlib links point to
matplotlib.org, and fixed a link in the notebook help menu to point to
our new notebook.html, now that htmlnotebook.html is a redirect.

Whoever ends up merging this PR should backport it to 1.x.
Fix test_map_iterable() again
Add test for IPython.start_kernel()
Merge pull request #4017 from gmbecker/PR_rmagic2

Add REPL-like printing of final/return value to %%R cell magic
Merge pull request #4018 from takluyver/tempdir-warning

Fix warning when running IPython.kernel tests
Merge pull request #4022 from ivanov/doc-links

DOC: fix links to matplotlib, notebook docs
Merge pull request #4021 from samuela/master

Fix parallel.client.View map() on numpy arrays

closes #4020
Merge pull request #4016 from takluyver/IPython-start-funcs

Fix IPython.start_* functions

start_kernel() didn't work at all (#4005), and I found while investigating that passing user_ns to either start_ipython() or start_kernel() had no effect, because the Application wasn't passing it on to the Shell.

This is a simple fix for the most pressing issues. We should think about any other parameters that we want to be passed through from our top level API, e.g. possibly user_module.

closes #4005