> The program does not parse some *.js files correctly. It 
> changes these files so they work incorrectly. How can I 
> switch parsing these files off?
Err you can disable the "dirty parser" using 'Set 
options' / 'Scan' and uncheck 'Attempt to detect all links'

This should be sufficient.

The other (and harder) workaround would be to add the 
following filter rule:
-*.js

(but this will rewrite all js links to external ones, which 
is not really good)