incorporate manual into deploying docs

[Tieqiong]

Also see #177

Now user guide (or often referred to manual) is merged into the cookiecutter api document and will be deployed with a certain url. Resources used in manual and tutorial will also be deployed.

[sbillinge]

This looks fine, but I see a bunch of doc/tutorial files simply deleted. What is the plan for these?

[Tieqiong]

So I guess when people follows the manual or tutorial it's easier for them to download resources for each section instead of individual resources, file by file (there are data series for one fit that people might have to download ~15 individual files for one example)

I compressed the doc/tutorial files by section as zip and put them in doc/source/manual_resources. You can check the name and see if we want to refine any of them.

[sbillinge]

So I guess when people follows the manual or tutorial it's easier for them to download resources for each section instead of individual resources, file by file (there are data series for one fit that people might have to download ~15 individual files for one example)

I compressed the doc/tutorial files by section as zip and put them in doc/source/manual_resources. You can check the name and see if we want to refine any of them.

Ok, that makes sense. When you make decisions like that, please start a comment chain so it can be discussed. In general more discussion of what you are doing and why would be helpful in your PRs