My friend is writing some documentation and asked me an English question I don't know the answer to. In this case which would it be?
CCleaner has been run.
CCleaner has been ran.
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It is being used with a perfect tense (has been, which usually means present perfect progressive, but not always - see below), so it requires the past participle (for completed action) or present participle (for continuous/still commencing action).
Additionally, your sentence is phrased in the passive voice (because CCleaner is not the agent in the sentence, it was run by something else). In the passive voice an auxiliary (usually) BE verb is used, which is used to give the tense (which would have been given by the main verb in the active voice), and this also requires the past participle of the main verb. Your sentence is using the present perfect tense in the passive voice. If it were not in the passive voice, it would require the progressive, present participle form if been is kept.
In the case of the verb run, the past participle is run and the present participle is running.
Run is an irregular verb with the following forms:
Infinitive / imperative / present - run (third-person singular runs)
Past - ran
Continuous forms with be / gerund / present participle - running
Perfect forms with have / passive forms with be / past participle - run
So you never should say have (been) ran or has (been) ran, it's always have (been) run or has (been) run.
That being said you will hear native speakers get it wrong all the time, especially when the speaker wants to emphasize has run.