yes, there is a huge cost, which is why step 1 needs to be "get the use cases" and step 2 needs to be "verify the user cases". This shouldn't be phase 3 but phase 1.
It sounds like you've inherited a system which has probably been set-up horribly, you should get it marked for replacement with a new system ASAP. For a stop gap, you could look to start writing simple scripts to do what is required and place them in a separate directory that is added to the PATH environmental, but I'd still look to get the system replaced by something on a priority basis if the permissions you have inherited were already too open.
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