In our shop there are two directories of code: src and bin. The classic mistake is altering something in the bin directory and then swearing when you overwrite it by doing make install.

On a slightly different note, do you find that moving from language to language introduces a lot of silly mistakes? I often switch betweeen TCL/TK and Perl, and end up forgetting ';' in Perl and putting too many '$' charaters in TCL.