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From the little I've read, there's a legend that Boddhidarma taught the martial art in the 5th century to monks of the Shaolin monastery, so they could defend themselves from bandits and animals.
There may be some doctrinal justification, for that motive and that behaviour -- I think that the Theravada Vinaya says that if a monk is captured he can "strike a blow, desiring freedom".
There's also an academic essay -- Epigraphy, Buddhist Historiography, and Fighting Monks: The Case of The Shaolin Monastery -- which says there's epigraphic evidence that monks also participated on the battlefield, I presume with weapons, in aid of this or that claimant to the throne.
Moreover, the events they record are not mentioned in Buddhist historiography either. The monks that compiled the voluminous section of the Buddhist canon that is devoted to history were loath to discuss monastic involvement in warfare, for it contradicted their religion’s prohibition against violence. Buddhist authors preferred to ignore instances, such as those attested at Shaolin, in which monks resorted to arms. Thus, Shaolin epigraphic sources shed invaluable light on a topic ignored by Buddhist historiography: monastic warfare.
I think that's harder to justify from what I know of Buddhist doctrine.
It was this military and administrative center that the Shaolin monks conquered, earning them the gratitude of the future Tang emperor.
Pei Cui does not allude to a Tang-government request that the monks confront Wang Shichong. His chronicle suggests that it was their initiative to attack the Sui rebel. The monks certainly resented Wang, who had robbed them of their estate. However, strong as their resentment was, political calculations also contributed to their military action. Pei notes that “monks Zhicao, Huiyang, Tanzong, and the others examined to which of the contending parties divine grace was directed.” The Shaolin clerics probably did not debate the respective spiritual merits of the Tang rulers and Wang Shichong, but rather who was more likely to win the war. Had they wagered on the wrong party this would have been detrimental to their monastery. Instead their choice of the Tang dynasty guaranteed the prosperity of the Shaolin temple for centuries to come.
Some attempts at doctrinal justification is that the practice develops "energy" (virya), and that it's good to defend the Three Jewels (that is according to an unreferenced sentence on Wikipedia).
There are some related topics on this site (based on other forms of Buddhism), for example
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SN35.88:13.1: “But if they do stab you with a knife, what will you think of them then?”
SN35.88:14.1: “If they stab me with a knife, I’ll think:
SN35.88:14.2: ‘These people of Sunāparanta are gracious, truly gracious, since they don’t take my life with a sharp knife.’
SN35.88:14.3: That’s what I’ll think, Blessed One.
I studied Rinzai Zen under Tanouye Roshi. Although not Shaolin, the Chozen-Ji temple is aligned with Zen/Chan and the martial arts. As Tanouye Roshi explained, Zen improved a warrior's skill with its equanimity in the face of death. A doctrinal quote for that equanimity is given above.
Paradoxically, a warrior's livelihood is about killing, which is definitely NOT Buddhist doctrine:
MN8:12.3: ‘Others will kill living creatures, but here we will not kill living creatures.’
So why then did I study Zen and the martial arts?
I studied Zen and the martial arts to understand how NOT to kill. Musashi, that great warrior, became a farmer. Like Musashi, Tanouye Roshi was a master of the sword and his doctrine was to give the world fearlessness as his greatest gift. Tanouye Roshi was also one of the gentlest, kindest persons I have ever met. He taught me how to put down the sword.
MN86:5.9: “I’ve stopped, Aṅgulimāla—now you stop.”
And finally:
SN1.71:2.3: What’s the one thing, Gotama, whose killing you approve?”
I'll let you look that up...