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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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test_example.txt
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=====================================
Tests in example form - pure python
=====================================
This file contains doctest examples embedded as code blocks, using normal
Python prompts. See the accompanying file for similar examples using IPython
prompts (you can't mix both types within one file). The following will be run
as a test::
>>> 1+1
2
>>> print "hello"
hello
More than one example works::
>>> s="Hello World"
>>> s.upper()
'HELLO WORLD'
but you should note that the *entire* test file is considered to be a single
test. Individual code blocks that fail are printed separately as ``example
failures``, but the whole file is still counted and reported as one test.