Keep comments after round-trip through AppComposer

## Problem
After opening a CloudFormation template in AppComposer, I find that all my inline comments have been wiped out and the document has be reformatted to remove any line breaks that I included for readability. It even did this without marking the document as `dirty`.

## Expected behavior
AppComposer should never modify and then save my document without some kind of opportunity to stop it. I would very much like it if AppComposer allowed me to keep my template comments as they frequently represent hard-earned operational knowledge that needs to be stored at the point of deployment.

Start by reproducing the round trip in AppComposer with a CloudFormation template containing inline comments and deliberate line breaks. Done means comments and formatting survive reopening and saving, or the user gets an opportunity to stop the modification before the document is saved and marked dirty.

Written by the indexing model from the issue text.