There were occasions during the war where "guerrilla companies" acted with regular Confederate forces. But they were under no particular discipline or regulation, and usually dispersed after a given raid, etc. General Jo Shelby used them as scouts, spies, etc. during his campaigns, and had no complaint of such services rendered.
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The Missouri Guerrilla commander William C. Quantrill evidently commanded a company of scouts, which acted occasionally with the army, and for this received the pay of a captain of "scouts" for such services rendered in 1862 and 1863...
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But generally his actions and operations were outside of any official authority, and perhaps too often transcended any of customary laws of war. Cole Younger, one of his chief lieutenants, in his memoir states Quantrill attempted to raise a large regularly organized partisan ranger command, but Richmond declined given some difference in opinion about the laws of war. He raised his force, apparently, anyways as a guerrilla force. Captain H.E. Palmer of the 11th Kansas Cavalry, USA, recalled of serving against Quantrill's guerrillas...
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But the Confederate army, and government, generally, wanted nothing to do with guerrillas in any official sense. There was provision in Confederate law for "partisan rangers" in regularly organized commands, operating beyond the lines, necessarily without pay, but these units were constrained to obey the laws of war so far as their circumstances allowed. Adam R. Johnson of the 10th Kentucky Partisan Rangers posted notice that his was not a guerrilla command, set upon thievery or vengeance, but a Confederate army unit...
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It became evident by 1864 some of even the partisan ranger bands had crossed the line into guerrilla disorder and the partisan ranger act was repealed, and any of their men that did not join regular commands were "outlawed" as deserters. Johnson's command, for example, being redesignated the 10th Kentucky Cavalry, CSA.
In August, 1864, for example, Adam R. Johnson addressed a note to the Union commander in Kentucky after two of his men had been shot as "guerrillas"... Johnson noting that holding his soldiers responsible for the murders of robbers or guerrillas in the vicinity was no more fair than blaming them for the killings by Indians...
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But the Union commander replied simply that as Johnson's command was acting outside of what were recognized as Confederate lines, he was constrained to act against anyone suspected of lawless depredations in a summary manner, irrespective of their claims of regular Confederate service, where evidence suggested the necessity.
In 1862, at the request of General Halleck in Washington, Francis Leiber prepared a treatise on the laws relative to guerrillas. He concluded partisan corps, where they acted as if lawless guerrillas, were not subject to treatment as prisoners of war. And guerrillas not at all.
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