С помощью history:
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$ history -cw
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См. --help:
[simterm]
$ history --help
history: history [-c] [-d offset] [n] or history -anrw [filename] or history -ps arg [arg...]
Display or manipulate the history list.
Display the history list with line numbers, prefixing each modified
entry with a `*'. An argument of N lists only the last N entries.
Options:
-c clear the history list by deleting all of the entries
-d offset delete the history entry at position OFFSET. Negative
offsets count back from the end of the history list
...
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