Your comments
Yeah you need to set that.
New release should sort out the css/template/drop-down issues. Good catches all around.
I'm hoping with the next Ubooquity release we can pull things in multiple ways, and then proper comic author/comic series/etc pages can be a thing. This was just to add a bit more functionality to the otherwise neglected Book section.
Edit: except the drop-down links needing to click the text, that I haven't sorted yet.
Edit2: nevermind, that's fixed in the comixology2.zip now too! :)
Do you have multiple base-shares, or is the only thing shared in comics your "comics" folder? If that's the case, there's a Ubooquity setting to "Bypass single root folder".
Series is the book-equivalent to story arcs, so if you don't use books it won't work for you.
Good catch on the css/template stuff, I'll sort that out soon.
And the adding/removing nav stuff is sorta hacky, I'll cut it back to just using Ubooquity settings (it's trying to be more user-specific, and apparently failing).
That's a weirdness with asynchronous loading (it appends whatever loads first first, etc), but should be less random once I incorporate caching.
Set the comicsBaseID to whatever your publisher page is (sounds like it's 1) and that'll get overridden with "Publishers". That'll also change the drop-down from Comics to Publishers.
There's an example publisher page here that shows all that's needed for publisher pages now. I streamlined it a ton.
theme.js was from the old theme, it's probably trying to be loaded by a folder-info.html in your publisher folder. Since in this version the publisher folder is theme-generated, you should delete that.
Ah yeah, sorry too quick on the trigger there.
So I'm thinking that the last big offender is the breadcrumb nav (Comics > blah > blah), since it does a lot of backtracking to figure out where you are in relation to other things (take current page, look at parent and find matching link title, go back one more and do it again).
I'll look at caching an array of page IDs, so it doesn't need to dive to find those.
For the homepage though, that's functionally loading 2-4 pages each time (new/random comics and/or new/random books). The idea of that is to actually show those, so I don't see a way to cache that. You could probably speed things up a bit by disabling the random pages (showRandom in themeSettings).
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You might want to edit the above, it's got your internet-facing url in it.