You misunderstand me - I agree that Licolns attitude was as described, I just happen to differ as to the legitimacy of his actions, which the Supreme Court also shared. The point being, why have a written Constitution if it can be shredded at will - or at least until Congress convened. After all, they can't convene themselves, it's up to the Executive to call them, which was (IMHO) much of the delay before they met. Given that Lincoln had a 2 1/2 month headstart they had little choice. Personally, I cannot fathom the worship of a President that ignored the Constitution, and basically made himself a dictator. If Presidents Washington or Reagan had performed similar actions, I would still feel the same.
And the branches might be co-equal, but that in itself does not allow one branch to place itself above the others. Ours is a system of checks and balances, and why have a written Constitution. James Madison (quoting Montesquieu), wrote in Federalist No. 47, that there "can be no liberty where the legislative and executive powers are united in the same person, or body of magistrates." The Constitution applies to Presidents in times of war, as well as in times of peace.
I really don't mean to divert from the habeus corpus question, which I gather is what you are thinking about. But please indulge me by answering this particular question about the letter which you cited. Do you agree with Lincoln that the Emancipation Proclamation was a normally unconstitutional act, made constitutional because necessary to the preservation of the Union (among other reasons, I presume)?