I'm wanting to focus on the Main Quest, but I want to join the civil war later on.

I'm at the point where the Jarl of Whiterun wants me to put an end to the war so he will let a dragon in his palace.

Will the truce end and allow me to join when I'm done with the main quest?

I believe if you are at that point, where a truce was signed (which is during the main quest line) then the truce stays in effect throughout the end of the game I believe. I do not think there is any way to break the truce after the point that you are at.

The truce is designed to halt the war until Alduin's defeat. After the MQ concludes, you'll be free to join either side.

The negotiations of the truce are some of the best dialogue in the game, IMO

define best... cicero and general thieves guild sounds great too me... esspecially Delvin Mallory (<3)
i guess in npc to npc chats, it is the best....

Difficult to say as there's no war going on even before it

Well, people talk about it, but it's just not there

Ok, I've got one post saying that the civil war is done forever, one post saying I can do the civil war after the main quest, and three that don't even answer the question at all.

Which is it? Is the truce permanent or not?

having just completed the MQ with the truce in place and then joining the stormcloaks AFTER defeating Alduin i can confirm that you can continue the civil war just fine after the MQ

Two of possibly my least favorite people in the Elder Scroll universe; next to Martin and any Thalmor.

If u do the truce u cannot join either side at all UNTIL alduin is defeated, then u can join. But not before alduin is defeated.