Update custom.js

Explain different semantics required for instances versus functions or classes. Based on comments of @minrk in #5985.
Update custom.js
Load rpy2.ipython for rmagic, print deprecation warning
Remove rmagic tests
Remove rmagic docs

Leaving intersphinx link to rpy2 docs.
No need to check for rpy2 in test machinery
Docs fixes for rmagic deprecation
Add URL to warning about rpy2
close websocket connections on ping/pong timeout

we recently added ws pings for keep alive,
and we can now use the longs to close dead connections.

This can apparently happen when connections are not closed cleanly,
e.g. on VPNs.

Setting ws_ping_timeout = 0 disables the ping mechanism altogether.
Add Math display support for qtconsole
Allow output prompt to leave out numbers for qtconsole
fix directory listing with broken symlinks

directory listing would 404 if any listed file doesn't exist
(e.g. symlink to missing target).

Previously-failing test included.
add secondary `debug` flag for heartbeats

in both KernelRestarter and parallel HeartMonitor

Since these both produce a huge amount of output,
they limit the usefulness of `--debug` output for debugging
other aspects of IPython.
test for overly greedy completion swallowing
fix for underscore completion
Make installation of native kernelspec explicit

Instead of creating a kernelspec directory matching the running
frontend, return its spec without writing to disk.

Adds a command 'ipython kernelspec install-self' to write a kernelspec
for the current version of Python.
Simplify kernel manager code
update mathjax CDN url in nbconvert template
update regex
refer to rlcompleter orginins

@minrk said it would be the prudent thing to do