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environment fixes in run #3191
Code in #3172 which adds --ignore-environment to dev-shell is redundant because --ignore-environment is already implemented for run. I moved the related code in run to a separate function. If doing it this way works, I was thinking I could move it to a common class that both run and dev-shell can inherit from.
I also changed the way ignore environment is handled, creating a new char* array if ignoreEnvironment is set rather than calling clearEnv. The previous way of doing it had to getenv, clearenv, and setenv for every kept variable, and clearenv for all variables, so it seems like creating a new array might be a better way of doing it that just does one getenv for kept variables. Not sure if it makes the call to runProgram and handling of PATH too complicated.