What was the impact of the Civil War on civil liberties?

One of the great debates in any democracy in crisis is whether individual rights should be sacrificed in exchange for national security. More recently, this became a subject of contention after the 2001 terrorist attacks on New York and Washington D.C. Abraham Lincoln was faced with similar rancor for his decisions during the Civil War.  There were actions that Abraham Lincoln took as commander-in-chief that abridged civil liberties of American citizens. The biggest coup during Lincoln's administration was the institution of military tribunals to try citizens. Martial law was also declared.  This means that civil authorities mus cede authority to military institutions.  These actions denied Constitutional protections of due process of law and the rights of trial by jury. His actions were also violations of the constitutional principle of habeas corpus. First Amendment rights of freedoms of the press and speech were also curbed during the Civil War.  These were drastic measures that would be unimaginable by today's standards.  

The stakes were very high for Lincoln. If the North did not win the war, the Constitution would be rendered meaningless. For this reason, Lincoln viewed it as pointless to protect constitutional rights at the expense of winning the war.