Research so far: I have combed through Wikipedia's article on "Habeas corpus in the United States (http://en.wikipedia.org/wiki/Habeas_corpus_in_the_United_States)", my own books on the Civil War, my school's databases and Google searches for various iterations of habeas corpus, Civil War prisoners, and anything else I can think of (I'm having trouble putting this into Google search terms). Most of what I have found has to do with Guantanamo Bay, which doesn't really apply, I think, because my character is an American citizen, arrested in the United States, for a political reason, rather than as an enemy or unlawful combatant.
Background: My character is spending several years in prison. She wrote a series of essays very critical of the government, appeared at a number of protests, and was finally arrested after a verbal altercation with a police officer. The protest and cause turned into a violent rebellion, which led Congress to suspend habeas corpus (per Art. I, Sec. 9, Cl. 2 of the Constitution). This is just the first part of a longer story, and I'm basing the general proceedings on the suspension of habeas corpus during the American Civil War.
The question: I'm having trouble figuring out what happened to all the Copperheads and Confederate sympathizers at the end of the Civil War. When the rebellion is over, and my character's side has lost, how will she get out of prison? I'm assuming that the suspension of habeas corpus will end, at some point, either by expiring or Congress passing another law. She has not technically committed any crime for which she can be prosecuted, but will she automatically be released? Or will she have to acquire legal counsel and/or file her own motion to secure her release? I found a couple of references to Presidents Lincoln and Johnson commuting certain individuals' sentences; in that case, would she have to apply to the President directly?
Any help would be much appreciated! I know there isn't that much historical precedent for this, but I'd like to make it as realistic as possible.