Lincoln, as President, was NOT ALLOWED to suspend Habeas Corpus under Article I, as you claim.
Article I defines the responsibilities of the LEGISLATIVE DEPARTMENT. Only the Congress has the authority to suspend Habeas Corpus as quoted in Article I.
Article II defines the authority of the EXECUTIVE DEPARTMENT!
Lincoln had no authority to suspend Habeas Corpus under our Constitution, however Paisan was correct in stating that Lincoln was pretty adept at ignoring those portions of the Constitution that were "inconvenient" to a war-time President.
Correct. So the problem wasn't that Habeas Corpus was suspended but that the Executive branch did it.