It should be noted that Lincoln delegated the authority to suspend habeas corpus to military officers who delegated further along the military chain of command. It was NOT Lincoln who suspended the writ in the case of Merryman but General Keim in Pennsylvania IIRC.
Congress authorized the suspension of the writ in 1863. The indemnity act did not declare prior acts regarding habeas corpus legal, but provided a legal shield (indemnity) against criminal prosecution or civil lawsuits. Such protection was given to Lincoln and all those who carried out his policy.
The Act of 1863 contained certain requirements and restrictions. In Ex Parte Milligan, the Court held that those requirements had not been complied with and found for Milligan 9-zip on the grounds that the Government action was unlawful. By a majority decision, the Court further held that the Milligan trial, (and all other such trials) was unconstitutional. It is unconstitutional to try a civilian by a military court when the civilian courts are operating normally.
Below is the beginning of my post reviewing the Congressional action. The complete post, including quotes of the Congressional debate, with links to the Congressional Globe, is available here:
http://www.freerepublic.com/focus/f-news/953533/posts?page=566#566
U.S. Supreme Court
THE AMY WARWICK, 67 U.S. 635 (1862)
THE BRIG AMY WARWICK.
THE SCHOONER CRENSHAW.
THE BARQUE HIAWATHA.
THE SCHOONER BRILLIANTE.
December Term, 1862
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Mr. Justice GRIER.
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And finally, in 1861, we find Congress 'ex majore cautela' and in anticipation of such astute objections, passing an act 'approving, legalizing, and making valid all the acts, proclamations, and orders of the President, &c., as if they had been issued and done under the previous express authority and direction of the Congress of the United States.' Without admitting that such an act was necessary under the circumstances, it is plain that if the President had in any manner assumed powers which it was necessary should have the authority or sanction of Congress, that on the well known principle of law, 'omnis ratihabitio retrotrahitur et mandato equiparatur,' this ratification has operated to perfectly cure the defect.67 U.S. 635, 670-1
To begin, I wish to point out that this is a lengthy decision and the authors clearly were not champions of brevity for the sake of saving an old growth forest. I will make this point relevant in short order.
The Court appears to say that Congress passed an act approving, legalizing and making valid ALL the previous acts, proclamations, and orders of President Lincoln. Let us examine that quote more closely.
Congress [passed] an act "approving, legalizing, and making valid all the acts, proclamations, and orders of the President, &c.,as if they had been issued and done under the previous express authority and direction of the Congress of the United States."
I have emphasized one (apparently) very short portion of the Act of Congress as it was quoted by the Supreme Court.
Please notice the &c embedded in there. That is an old fashion abbreviation for et cetera. In this case, it denotes words omitted from the Act of Congress which was being quoted. I will now present the material with the missing words restored, as it appears in the official record of the time, The Congressional Globe. Notice how the "President, &c., as" expands.
Sec. 3. And be it further enacted, That all the acts, proclamations, and orders of the President of the United States, after the 4th of March, 1861, respecting the Army and Navy of the United States, and calling out or relating to the militia or volunteers from the States, are hereby approved, and in all respects legalized and made valid to the same intent, and with the same effect as if they had been issued and done under the previous express authority and direction of the Congress of the United States.
By my count, the Supremes took out 52 words. They did not do so for the sake of clarity, because the result is most certainly not a clarified version of the original. The debate in the legislature makes abundantly clear that the Act applies only to military appropriations and the callup of the troops. The debate assures that habeas corpus was specifically excluded from consideration by the Act.
Moreover, they did not excise the 52 words in an effort to save a tree.
The Act of Congress which passed was a bill (S. No. 72) "to increase the pay of the privates in the regular Army, and of the volunteers in the service of the United States, and for other purposes."
There was a proposed Joint Resolution (SR-1) "To approve and confirm certain acts of the President of the United States for suppressing insurrection and rebellion." This resolution died without a vote, and fell into such disfavor that by the end of the session its opponents were the one's clamoring for a debate on the resolution. On August 6, 1861, the last day of the special session, Illinois Senator Trumbull disposed of it before it could suffer an embarrasing vote of rejection.
On August 5, Senator Wilson attempted to introduce a new bill, S-70, with the content quoted above. Senator Wilson noted that, "The bill avoids all questions with regard to the habeas corpus and other matters, and refers simply to the military appropriations; and it is necessary we should do this in order to place that subject upon the right ground." ... "It takes but a single point, and avoids the points of debate in the joint resolution that was before the Senate, and simply legalized the action of the President which we have already indorsed, by giving him the authority. It refers merely to a point which it is very necessary for us to consider."
And you took out these:
"By the Constitution, Congress alone has the power to declare a national or foreign war. It cannot declare was against a State, or any number of States, by virtue of any clause in the Constitution. The Constitution confers on the President the whole Executive power. He is bound to take care that the laws be faithfully executed. He is Commander-in-chief of the Army and Navy of the United States, and of the militia of the several States when called into the actual service of the United States. He has no power to initiate or declare a war either against a foreign nation or a domestic State. But by the Acts of Congress of February 28th, 1795, and 3d of March, 1807, he is authorized to called out the militia and use the military and naval forces of the United States in case of invasion by foreign nations, and to suppress insurrection against the government of a State or of the United States."
Walt