Not trying to be argumentative, but from what I see in the official records about supply for this timeframe, but I don't really see Halleck, or anyone else, involved in a concealment of a crisis.
Drawing on Stotelmyer,
Too Useful to Sacrifice:
On October 2nd and 3rd the supply situation is bad enough that there's a food riot in the 9th NY (the Hawkins Zouaves) and reports indicate that the situation is certainly not good:
Another I Corps officer, General Patrick, also remarked on the troops’ condition: “The Officers and men are without clothing . . . are ragged and filthy. Many of them have vermin upon them & cannot get rid of them.” Next day he noted, “Our men are poorly prepared for storms. Their Shelter Tents are worth very little for protection, & they (the men) are getting very weak & unable to endure much exposure . . . I am sending everywhere for tents, but do not get them.”
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 238). Savas Beatie. Kindle Edition.
In later sections:
Throughout much of October McClellan constantly complained that his requisitions for supplies had not been met, consequently it was impractical, if not impossible for him to advance into the enemy’s country. Traditional accounts of Civil War history contend that this supply crisis did not exist, and that everything McClellan asked for was supplied. This same literature insists that McClellan’s hesitancy to advance after the battle of Antietam was “in consequence of a constitutional indecision and want of vigor.”65 A close examination of the primary sources reveals quite a different picture. On October 7, one of Meigs’ quartermasters, Lt. Col. C. G. Sawtelle informed
Ingalls, “I have ordered the clothing called for by your dispatch of to-day to Hagerstown.” Hagerstown was at least 10 miles north of Sharpsburg, which was almost a full day’s travel by horse and wagon. The logistical problem by October was that most of the army had moved at least 10 miles south of Sharpsburg to the Harpers Ferry area. The journey to Hagerstown and back was thus a time-consuming endeavor. “The Quartermaster-General thinks he can furnish all the clothing and camp equipage that may be required for the Army of the Potomac,” Sawtelle wrote. “There may be some delay in the matter of blankets and shoes and stockings.” A frustrated Ingalls shot back, “It is a matter of grievous complaint that the clothing and other supplies ordered do not arrive at Harper’s Ferry . . . See where the obstacles are.” Harpers Ferry was on the direct line of the B&O. Why were supplies being sent to Hagerstown?
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 244). Savas Beatie. Kindle Edition.
By October 11 McClellan directly called Halleck’s attention to the situation. “We have been making every effort to get supplies of clothing for this army and Colonel Ingalls has received advices that they have been forwarded by railroad, but . . . they come in very slowly.” Later the same day he wrote, “I am compelled again to call your attention to the great deficiency of shoes and other indispensible articles of clothing that still exists in some of the corps of this army.” McClellan told Halleck the War Department had assured him clothing would be forwarded. “Corps commanders sent their wagons to Hagerstown and Harper’s Ferry for it,” he continued. “It did not arrive as promised, and has not arrived yet . . . The men cannot march without shoes.”
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 245). Savas Beatie. Kindle Edition.
On October 19, Sgt. Benjamin Hirst, of the 14th CT wrote to his family:
About the middle of October . . . Sent in requisitions for Shoes and Clothing, and sent to Washington for our knapsacks, but we were destined to never see them again. There has been so much said about McClellan, having everything sent to him, that the army required, that it has since disgusted me with the Lying statements made in the Party Newspapers we had never yet got what belonged to us, our requisitions for clothing were unheeded because the Quartermaster had them not . . . it was sheer Humbug at this time, to say the army had everything they wanted . . . I had 2 shirts on my back, a Stolen Overcoat, and was a share holder in a Rebel blanket, a fine assortment for a Winter Campaign . . . there were other ones worse of[f] than me.
Hirst’s account to his family was not exaggeration. On the same day a correspondent for the New York Herald observed, “They [the army] have not received their fall clothing, are destitute of blankets, tents and raincoats, in fact of all kinds of Quartermaster’s stores.
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 247). Savas Beatie. Kindle Edition.
During much of October Meigs and Halleck are being informed of the deficiencies. Meigs says that the requisitions have all been promptly filled and dispatched, but:
Overwhelming evidence argues otherwise. On October 23, the interim commander of the I Corps, Brig. Gen. George G. Meade, wrote his son John. “We are in hourly expectation of marching orders . . . We have been detained here by the failure of the Government to push forward reinforcements and supplies,” he explained
“You will hardly believe me when I tell you,” he continued, that as early as the 7th of this month a telegram was sent to Washington informing the Clothing Department that my division wanted three thousand pairs of shoes, and that up to this date not a single pair has yet been received (a large number of my men are barefooted) and it is the same thing with blankets, overcoats, etc., also with ammunition and forage. What the cause of this unpardonable delay is I can not say, but certain it is, that some one is to blame, and that it is hard the army should be censured for inaction, when the most necessary supplies for their movement are withheld, or at least not promptly forwarded when called for.”
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 249). Savas Beatie. Kindle Edition.
Alpheus S. Williams, October 26:
We want shoes and blankets and overcoats—indeed almost everything. I have sent requisition upon requisition; officers to Washington; made reports and complaints, and yet we are not half supplied.
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 249). Savas Beatie. Kindle Edition.
The clamor over supplies caught Lincoln’s attention, and he sent Col. Thomas A. Scott, former assistant secretary of war, on a fact-finding mission to evaluate McClellan’s complaints firsthand at his headquarters near Harpers Ferry. “About the middle of October 1862,” he recalled, “I had a conversation with Mr. Stanton, Secretary of War, and President Lincoln, in regard to the delay in the movement of General McClellan’s army, and its reported condition of inefficiency to effect a movement without proper and greatly needed supplies.” McClellan told Scott the matter did not require discussion—he would have one of his staff “show me the requisitions . . . for supplies, and also a statement of the amount received, and that I could draw my own inferences.” Scott verified a shortage of “shoes, clothing, and other necessaries for the men.” Satisfied, Scott returned to Washington and reported his findings to Lincoln, Halleck, and Stanton:
Both Mr. Stanton and General Halleck then repeated their assurances that all General McClellan’s requisitions had been met; and it was suggested that, as the troops in the forts around Washington constituted a part of the Army of the Potomac, the supplies that were intended for General McClellan’s army in the field, instead of having been sent to him at Harper’s Ferry, had
by some means or other [emphasis added] been diverted for use of the troops in the fortifications, and thus had failed to reach him. This proved to be the explanation of the trouble.
Stotelmyer, Steven R.. Too Useful to Sacrifice (pp. 250-251). Savas Beatie. Kindle Edition.
In short, the supplies were needed, the requisitions were sent for, and for weeks nothing arrived. Halleck kept saying there was no problem, and when finally confronted repeated his claim that there was no problem, but suggested that maybe the supplies for about a hundred thousand men had been sent to the Washington fortifications.
Halleck said for the record that in his opinion supplies were not lacking in McClellan's army. When asked by Stanton:
“Requisitions for supplies to the army under General McClellan are made by his staff on the chiefs of bureaus here,” Halleck’s responded the next day. “No such requisitions have been, to my knowledge, made upon the Secretary of War, and none upon the General-in-Chief.” Having covered both himself and Stanton, in typical fashion the general waffled, admitting that on “several occasions General McClellan has telegraphed to me that his army was deficient in certain supplies . . . there has not been, so far as I could ascertain, any neglect or delay in issuing all supplies asked for by General McClellan or by the officers of his staff.” Halleck failed to mention that he did this from his desk, not the field. From the information he had, Halleck opined, that “requisitions from that army have been filled more promptly, and that the men, as a general rule, have been better supplied than our armies operating in the West.”
Stotelmyer, Steven R.. Too Useful to Sacrifice (pp. 256-257). Savas Beatie. Kindle Edition.
He also said:
"There has been no such want of supplies in the army under General McClellan as to prevent his compliance with the orders to advance against the enemy.”
Stotelmyer, Steven R.. Too Useful to Sacrifice (p. 257). Savas Beatie. Kindle Edition.
In short:
1) There was a supply shortage, as well attested to by overwhelming evidence.
2) Halleck claimed that he had investigated and found there was no supply shortage.
Therefore, in the best possible interpretation Halleck is saying things he cannot verify are true (and thus helping to conceal the supply crisis).
What seems to have been going on in the ORs is either a case of bureaucratic stonewalling (i.e. acting like nothing was wrong), CYA to avoid blame for a massive SNAFU where supplies didn't reach McClellan until about the 22nd of October (a special wagon-train full of shoes were sent that day) or active denial of resources. By themselves, they of course seem to indicate everything is going well, but they have to be contrasted with the essentially incontrovertible fact that there was a massive shortage of clothes, shoes, horses etc. in the Army of the Potomac - and that means that claims that "everything is going well" in the ORs are misinformed or lying.
Any other explaination is to claim that three corps commanders (AS Williams, FJ Porter, George Meade), various soldiers from private to colonel and Joseph CG Kennedy (a member of Lincoln's retinue) were all fabricating information on the supply-poor and particularly clothing-poor state of the Army of the Potomac.