The whole thing; not concealing the less attractive parts.
This phrase is said to derive from Oliver Cromwell's instructions to the painter Sir Peter Lely:
Oliver [Cromwell]... said to him, 'Mr Lely, I desire you would use all your skill to paint my picture truly like me, and not flatter me at all; but remark all these roughnesses, pimples, warts and everything as you see me, otherwise I will never pay a farthing for it.'
At the time of the attributed instruction, Cromwell was Lord Protector of England. Lely had been portrait artist to Charles I and, following the restoration of the monarchy in 1660, he was appointed, in 1661, as Charles II's Principal Painter in Ordinary.
Lely's painting style was, as was usual at the time, intended to flatter the sitter. Royalty in particular expected paintings of them to show them in the best possible light, if not to be outright fanciful. This portrait of Charles II shows what was expected of a painting of a head of state in the 17th century.
Despite a preference for being portrayed in his portraits as a gentleman of military bearing Cromwell was well-known as being opposed to all forms of artifice. This 'puritan Roundhead' versus 'dashing Cavalier' shorthand is often used to denote the differences in style of the two opposing camps in the English Commonwealth and subsequent Restoration. It is entirely plausible that he would have issued a 'warts and all' instruction when being painted. It would certainly have been necessary for someone to have told Lely to modify his style in order to produce the warty portrait that he did in fact provide for Cromwell.
We have Cromwell's death mask as a reference. From that it is clear that Lely's portrait is an accurate record of Cromwell's actual appearance.
Despite the plausibility of the account there doesn't appear to be any actual evidence that Cromwell ever asked to be painted 'warts and all. The first record of that phrase being attributed to him comes from Horace Walpole's Anecdotes of painting in England, with some account of the principal artists. That was published in 1763 - over a hundred years after Lely painted Cromwell. Walpole included no evidence to support the attribution, nor any explanation of why no one else had mentioned the phrase in the preceding hundred years. We can only assume he was indulging in a piece of literary speculation rather than historical documentation.