Familiar problem, but I learnt to cope with it in a very early stage the hard way...
I named a Perl script plainly "test" and thought to execute is by typing "test" in a bourne shell. It was only one hour later that I learnt about the shell builtin test and to always prefix a local script/program name with a dot-slash, like "./test" or whatever. On a side note, on unix, user root shouldn't even have the working directory in its PATH for security reasons...
By always explicitly invoking the command in the (current) directory you shouldn't get too many surprises IMHO (and yes, using a real version management system is the way to go - familiarising oneself with the somewhat arkane CVS syntax pays very much in the longer run).
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