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Here's a nice little excerpt from the record of proceedings in the full panel hearing (minus Merrick, of course, who was under house arrest) of the D.C. Circuit Court over the case of Murphy v. Porter. They demonstrate conclusively that Lincoln's dirty hands were all over Porter's activities.

AT LAW: The Marshal of the District was directed not to execute the writ upon Provost-Marshal Porter, and to make return. That he was ordered by the President of the United States not to serve the same, as the writ of habeas corpus had been suspended as regards soldiers in the army of the United States, within said district, by the order of the President.
... PROCEEDINGS FOR OCTOBER 21, 1861 (note - the referenced letter from Judge Merrick is excerpted in DiLorenzo's article):

The reading of the communication (from Judge Merrick) having been concluded, Judge Dunlop announced that the two remaining Judges (himself and Judge Morsell) had, after consultation, decided that the letter should be filed as requested by Judge Merrick, and it was so ordered.
They also thought it might, as the writ (of habeas corpus) had been regularly issued, to state that the matter was now before the Court to be tried.
The statement of their brother Judge presented a case where the progress of law is obstructed. It was the duty of the Court to afford the remedy, and, if the facts are as stated, to cause the law to be respected.
As the Provost-Marshal had obstructed a process of this Court, it would order a rule to be served on General Andrew Porter, to appear before the Court and show cause why an attachment for contempt should not issue against him.
Judge Morsell said that this was a palpable and gross obstruction to the administration of justice, to prevent a Judge of this Court from taking his seat because he issued a writ just such as the law requires.
The placing of a sentinel before Judge Merrick's house was evidently for the purpose of embarrassing him in this particular subject, and to prevent his appearance in Court.
He (Judge Morsell) would make the rule broader so as to have the Provost satisfy the Court as to both matters. The Court has its duty to do, a duty the Judges are sworn to do, and that duty is the administration of justice according to law.
What is the real state of things? If martial law is to be our guide, we look to the President of the United States to say so. He (Judge Morsell) did not pretend to controvert the right of the President to proclaim martial law, but let him issue his proclamation. The Judges have their duty to do under the law, and are liable to be punished if they do not do it. I intend to do my duty, and vindicate the character of this Court as long as I sit here. I am an old man. The following notice was written off by the Judge: In the Circuit Court of the District of Columbia The Clerk is directed to file the letter of Judge Merrick, addressed this day to the Chief Judge of the Court. And it is ordered this 22d day of October, 1861, that a rule to show cause be issued against General Andrew Porter, Provost-Marshal of the District of Columbia, requiring him, on or before the 26th of October, 1861, to show cause to this Court why an attachment of contempt should not issue against him for obstructing the process and course of justice and administration of it in this Court, in the particulars set forth in Judge Merrick's letter, that a copy of said letter accompanying the rule to show cause, and that the same be returnable on Saturday, the 26th of October, at 10 A. M. of that day, at the Courtroom in the City Hall, Washington. By order of the Court. Test. JOHN A. SMITH, Clerk.

Let's recap what has happened so far. First, Murphy's father petitioned the court for a writ of habeas corpus on behalf of his son, an underage minor being held to service in the union army. Judge Merrick recieved the case and issued the writ of habeas corpus for Murphy, delivering a copy to Murphy's attorney (Foley). Shortly thereafter Foley delivered a copy of the writ to Provost Marshall Porter, who subsequently refused it and had Foley himself imprisoned. Later that evening when Judge Merrick returned home he found that Porter had stationed armed sentinels at his house placing him under house arrest and preventing him from attending the full circuit's panel as the case advanced. Merrick sent notice of this situation to the court, which convened in his absence to hear the case. Finding that Porter had obstructed the process of justice by preventing Merrick's presence, the court ordered Merrick's letter entered into the record and a summons issued to Porter to show cause as to why he should not be held in contempt for his actions. The panel, absent Merrick, convened again to deal with the arising contempt case over Porter only to find that he had shunned the summons to show cause as well. That is where we pick up now...

In the Circuit Court on Saturday, October 26, 1861, Judges Dunlop and Morsell being present:
The Court asked the clerk if there had been any return to the writ issued against General Porter, the Provost-Marshal of this city.
The clerk answered there was none.
Mr. Carrington, the District Attorney, presented in behalf of the Deputy-Marshal (Mr. Philips) a paper, with the affidavit of Mr. Philips, stating that the rule had not been served, because he had been ordered by the President not to serve it, and because the privilege of the writ of habeas corpus had been suspended for the present by the President, in regard to soldiers in the army of the United States, within the District of Columbia.

As you can see, Porter's response through one of his henchmen was blunt in its disregard of the court. He told them point blank that he didn't have to acknowledge their orders and contempt proceeding because Saint Abe had authorized him to act as he did! Next we go to the ruling of the court, which, though strongly worded, went ignored by Saint Abe and his henchmen just like Merryman and at least three other federal court rulings against Lincoln over habeas corpus. You will also note that, just like the case heard by Taney, Lincoln provided absolutely no notice of his many orders to the court until AFTER the case had arisen

Judge Dunlop, after holding the above under advisement announced he decision of the Court in the case, as follows:
The return made by Deputy Marshal the 26th of Oct., 1861, we will order to be filed, though we do not doubt our power to regard it as insufficient in law, and proceed against the officer who has made it.
The existing condition of the country makes it plain that that officer is powerless against the vast military force of the Executive, subject to his will and order as Commander-in-Chief of the Army and Navy of the United States.
Assuming the verity of the return, which has been made under oath, the case presented is without a parallel in the judicial history of the United States, and involves the free action and efficiency of the Judges of this Court.
The President, charged by the Constitution to take care that the laws be executed, has seen fit to arrest the process of this Court, and to forbid the Deputy Marshal to execute it. It does not involve merely the question of the power of the Executive in civil war to suspend the great writ of freedom, the habeas corpus.
When this rule was ordered to give efficiency to that writ, no notice had been given by the President to the Courts of the country of such suspension here, now first announced to us, and it will hardly be maintained that the suspension could be retrospective.
The rule on this case, therefore, whatever may be the President's power over the writ of habeas corpus, was lawfully ordered, as well as the writ on which it was founded.
The facts on which the rule was ordered by the Court are assumed to be true as respects the President, because the President had them before him, and has not denied them, but forbade the Deputy Marshal to serve the rule on General Andrew Porter.
The President, we think, assumes the responsibility of the acts of General Porter, set forth in the rule, and sanctions them by his orders to Deputy Marshal Philips not to serve the process on the Provost Marshal.
The issue ought to be and is with the President, and we have no physical power to enforce the lawful process of this Court on his military subordinates against the President's prohibition.

In summary:
1. Judge Merrick issues a writ of habeas corpus to the attorney for Murphy, an underage minor being detained in the union army.
2. Provost Marshall Porter refused the writ, imprisons Murphy's attorney, and places Judge Merrick under house arrest to prevent his attendance at the circuit court panel on the case.
3. The circuit panel convenes, absent Merrick, and rules Porter to have obstructed the court's process. They summon Porter to show cause as to why he should not be held in contempt.
4. Lincoln personally intervenes and blocks the court's rule from being delivered to Porter. Porter's surrogate responds to the court notifying them of Lincoln's authorization for Porter's actions.
5. The court affirms its rule and strongly condemns the illegality of Lincoln's action but concedes that it is unlikely to be obeyed as Lincoln is employing a superior military power to obstruct the court from enforcing its rulings.