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promote aliases and flags, to ensure they have priority over config files...
promote aliases and flags, to ensure they have priority over config files add Application.flatten_flags() method, which adjusts the alias and flag dicts, such that they point to the subclass in the Application.classes list when passed to the argv parser. This prevents TerminalInteractiveShell.colors in a config file overriding `--colors` on the command-line, which points to InteractiveShell.colors. Flattening is only done when the answer is unambiguous, so multiply inherited classes (e.g. Launchers in ipcluster) are not touched. also remove now-obsolete manual workaround for this in IPClusterStart closes gh-849

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logtopics.rst
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MinRK
zmq kernels now started via newapp
r3970 =======================
Log Topic Specification
=======================
we use pyzmq to broadcast log events over a PUB socket. Engines, Controllers, etc. can all
broadcast. SUB sockets can be used to view the logs, and ZMQ topics are used to help
select out what to follow.
the PUBHandler object that emits the logs can ascribe topics to log messages. The order is:
<root_topic>.<loglevel>.<subtopic>[.<etc>]
root_topic is specified as an attribute