please read http://meta.wikimedia.org/wiki/Replace.py, there are a lot of funny and useful things.
Exceptions are your friends, either in command line or within a fix, if you use fixes.py or user-fixes.py.
All the exceptions are not correctly written at the moment, you will find the approximate list in the Italian or Hungarian version (top of the page), but I tell you, link is the exception for all internal inks, including interwiki and categories, and interwiki just for interwikis.

2011/10/4 W Chaipau <wikichaipau@gmail.com>

I downloaded pywikipedia yesterday and am using it on the Assamese Wikipedia.  Thanks for a great product! 

Nevertheless, I have a little difficulty trying to make it do exactly what I want.   I am using it to correct some unicode encoding issues.  In particular, I am trying to replace some unicode characters by some others.  They are very short: at most 3 characters long. 

But I have been unable to avoid picking up matches inside wikilinks (internal as well as inter-language).  Is there a way to do so without employing unicode regularization? 


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