More than one of your possibilities is legal, and I'll go thru them one by one. At the end I'll offer a counter-suggestion.
First though, is the command called whole extraction? Is there a partial extraction command? If not, just leave off the word whole altogether. It is both unnecessary and confusing. Since I do not know the context, maybe it is necessary. I'm just saying it looks out of place. Should it be significant, use quotes ("whole extraction") or italics (whole extraction) to indicate to ignorant folks like me that whole is not being used in an informal speech manner (as in the whole shebang).
Second, is this even a "command"? Commands are most often verbs. I can see "whole extraction" as being a command line option more than a command itself.
Note that I have inserted commas to divide the two primary clauses, each of which could stand on their own.
- The whole extraction command is optional, and if it wasn’t specified, no extraction is performed.
- The whole extraction command is optional, and if it wasn't provided by the user, no extraction is performed.
Mismatch with the original "is". You could get away with it though if you changed the final clause to use "would be performed". The difference between "specified" and "provided by the user" is insignificant.
- The "whole extraction" command is optional, and if it hasn't been specified, no extraction is performed.
- The "whole extraction" command is optional, and if it hasn't been provided by the user, no extraction is performed.
These are better. The "is" no longer conflicts with "if it has not been".
Even better would be to break up the sentence. One can use three clauses in a sentence, but why? You are already talking about something technical. Further barriers to comprehension just get in the way. I would write it as:
- The extraction command is optional. When it is not specified, no extraction is performed.
Also note that the three instances of "is" completely track with one another. Present, past, future, intervening events -- all irrelevant to the general operational guidance you are providing. (The words "it is" are optional; when absent they would be understood.)