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Note that the "Running with irrigation" page has the same issue in the Latest Development Code version of the User's Guide, but not the CLM5.0 version. (I suspect the "Custom crop calendars" page would exhibit this same behavior, but it didn't exist in CLM5.0.)
Simplest thing might be to just lowercase all the filenames of pages experiencing this issue. It would be nice to know why this is happening, though...
E.g., if in the sidebar you click on 1.5.4 (Running with custom crop calendars), you're taken to https://escomp.github.io/ctsm-docs/versions/master/html/users_guide/running-special-cases/Running-with-custom-crop-calendars.html which gives a 404 error. The actual URL should be https://escomp.github.io/ctsm-docs/versions/master/html/users_guide/running-special-cases/running-with-custom-crop-calendars.html—note lowercase at the front of the HTML filename, even though the .rst file is capitalized.
Note that some capitalized filenames work fine, like https://escomp.github.io/ctsm-docs/versions/master/html/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.html.
There doesn't seem to be a difference in how the filenames are linked in their respective index.rst files: broken, working.
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