Farber, pg 194-195:
"An 1863 statute [Habeas Corpus Act] provided that 'any order of the president, or under his authority, amde at any time during the existence of the present rebellion, shall be a defense in all courts to any action or prosecution ... for any search, seizure, arrest, or imprisonment.' The statute also gave the defendant the power to remove state litigation to federal court and provided a two-year statute of limitations (even if the case remained in state court) for any action brought against an officer acting 'under color of' presidential or congressional authority.
"The Supreme Court upheld this statute in Mitchell v Clark. When the Civil War began, the Court explained, no legal authority had existed to deal with dangerous, disloyal individuals, thus requiring officials to take extralegal action. 'For most of these acts there was a constitutional power in congrss to have authorized them, if it had acted in the matter in advance.' In addition, perhaps, 'in a few cases, for acts performed in haste and in the presence of an overpowering emergency, there was no constuitutional power to make them good.' The Court had no doubt about the validity of the statute: 'That an act passed after the event, which, in effect, ratifies what has been done, and declares that no suit shall be sustained against the party acting under color of authority, is valid, so far as congress could have conferred such authority before, admits of no reasonable doubt.' For 'these are ordinary acts of indemnity passed by all government when the occasion requires it.'"
Short version: retrospective authorizations actions made by Congress are valid (this was also the conclusion in the Prize Cases); actions taken by Lincoln, and retrospectively authorized by Congress, are also valid.
"An 1863 statute [Habeas Corpus Act] provided that 'any order of the president, or under his authority, amde at any time during the existence of the present rebellion, shall be a defense in all courts to any action or prosecution ... for any search ...
Now stop right there, John Adams. Explain to me how Congress by itself has the power to overturn the Fourth Amendment.