All inline links broken in User's guide

[amfox37]

It seems like all the inline links in the User's guide referencing other sections of the document are broken? They are linking to CLM-URL. e.g. All on the intro page here I'm assuming they used to work, but don't know that for a fact...

[dlawrenncar]

Another user from the tutorial noticed this. We really need to resolve this issue soon, I think. Adding next label so we can make a plan.

[billsacks]

@ekluzek and I started working on this and got as far as fixing the links in the Introduction. The changes here should provide a template for the other changes that are needed. Fixing all of the links will likely be tedious: each link requires a search for the appropriate section title to link to, and since the user's guide has evolved somewhat, it isn't always immediately obvious what the correct section is.

I have pushed an in-progress branch to the main CTSM repo on ESCOMP to facilitate collaboration on fixing these links. The branch is named fix_doc_links. Here are the diffs so far: https://github.com/ESCOMP/CTSM/commit/40bf23816ca43bb102dbf1c469591c2a4c917dde .

A few notes:

• To find links, I searched for backticks (`); many can be found by searching for CLM-URL, but I don't think that picks up all of the links.
• I am using the ref syntax to give the links; the other option is to use numref, which gives the section number rather than its title; I thought that, in this case, giving the section title would be more useful. (@ekluzek note that this differs from what I first showed you.)
• The target of links is given by labels in the text that look like .. _running-single-points:. So far everything I have wanted to link to already has a label like that; if you find one that doesn't, you can add one with any unique label you want.
• In general, "Chapter 1" in old links seems to refer to 1.1, "Chapter 2" to 1.2, etc., but it seems like at least one new section has been added, because "Chapter 8" seems to refer to 1.9, the testing section.
• I am using the word "section" rather than "chapter" for consistency with other parts of the documentiation.
• Some broken links try to use dynamic variables like |version| in the link... that doesn't seem to work.