Fix chocolate-doom-git install procedure

Due to changes in the Chocolate Doom build system,
chocolate-common-git includes manual pages for all the individual game
setup programs. Removed these to resolve it.
Switch chocolate-doom-git clone URL from native Git protocol to HTTPS.

This is a bit more secure and not subject to MITM attacks.
Fix up the conflicts in chocolate-doom-git a bit.

Instead of having every package conflict with every main release
package, set them individually.

Ultimately this kind of doesn't matter since you can't have a mix of
both installed anyway, but it feels cleaner to me.