if all the tools are manually removed from default.conf
What makes you think you are supposed to edit that file?
interesting question. makes me wonder why xml is used at all if the files aren't robust to hand editing.
Makes me wonder why people seem to have a compulsory need to edit any file that contains xml. If it was a binary file, would you be urged to fire up the hex editor in the same way?
This has nothing to do with the question whether or not the config files are robust. I have edited my config file many times. That doesn't make it right, though.
We have had cases in the past where people have wasted hours of support time because of "bugs in Code::Blocks that made their build fail" and in the end it turned out they had modified their project files in an editor and just happened to have no clue what they were doing.
I am not saying that above poster doesn't know what he is doing, but this is a general thing. Project files and the config file are not to be edited by hand. Of course, you can still do it, but whatever happens is your own problem in this case.