Didn't realize you were unfamiliar. Okay, so in 1.9 Command Blocks got changed in a few ways with new settings and modes:
----Impulse Command Blocks: These are the same as the old ones, and behave as they did normally with the addition of the new settings.
----Chain Command Blocks: All command blocks now point in a direction, which help with these. If a command block is pointing into a chain command block, the chain command block will attempt to run its command as well if it has power.
----Repeating Command Blocks: These have a built in clock, and try to run their command every tick as long as they have redstone power.
----Conditional: This command block will only execute its command if the one behind it successfully executed its command.
----Always Active: This command block no longer needs Redstone, behaving as though it were permanently powered.
All of these new settings are very helpful for condensing command block creations if you know how to use them. The issue is the template parser does not recognize the new modes because they are new blocks, and it doesn't store the new settings or the commands of these new blocks because they are NBT data. When generating them, they only retain information stored as metadata. As such, to use them effectively, they must be manually inserted into the ruins file as "teblock"s so that the proper NBT data can be added.