Changing the representation of Section

[tingyuw]

Contributed to #2693, flatten the Section representation and removed nested structure. Stable files are changed because html is generated in a slightly different way. More changes need to be done later. Future works include:

1. TermsandDefs section consistency for GlassBR #1432 - I removed this section in GlassBR for now since we aren't able to generate it in the new structure, will add it back later after we address the issue.
2. Adjust higher level structure and language and use tree structure for Table of Contents, as discussed in #2915.

[tingyuw]

I'll fix the build failed in the next few days.

[balacij]

Was this just outdated? Do we need to keep the old branch?

[tingyuw]

@balacij Some of these changes are in another branch. I'm currently cleaning up my code, and I will delete this branch (all my branches) after I have merged everything into the master. I will clean up my tickets as well, don't worry:smile: