I am aware of the html manuals on the dev website.

Not officially, it seems.
https://ia801606.us.archive.org/22/items/shovel-knight-manual/shovel-knight-manual.pdf

*** A current Instruction Manual for "Shovel Knight: Treasure Trove" free to be downloaded! ***
    (139 pages and 6.2 MB - see developers OK for it at the end)

I am also a fan of manuals and thus I was eager to get it - but unfortunately the document above
was just a part of the Online Manuals provided by the Developers (i.e. not current).
Thus I created a new unofficial PDF manual for "Shovel Knight: Treasure Trove" using the current
online manuals and created one PDF document, which can be downloaded here:
https://www.jmb-edu.de/pdfs/Shovel_Knight__Treasure_Trove__All_9p1_Instruction_Manuals__20140617_to_20191207__JMB.pdf.

Here some kind of recipe (how I created this PDF):
 X Treasure Trove - entire set of 5 parts (p.1-4; 4 pp):
   o https://yachtclubgames.com/shovel-knight-treasure-trove-instruction-manual/
 1 Shovel Knight: Shovel of Hope (p.5-14; 10 pp):
   o https://yachtclubgames.com/instruction-manual/
 1p Shovel of Hope: Co-op Instruction Manual (p.15-23; 9 pp):
   o https://yachtclubgames.com/shovel-of-hope-co-op-instruction-manual/
 2 Shovel Knight: Plague of Shadows (p.24-43; 20 pp):
   o https://yachtclubgames.com/plague-of-shadows-manual/
 3 Shovel Knight: Specter of Torment (p.44-63; 20 pp):
   o https://yachtclubgames.com/specter-of-torment-manual/
 4 Shovel Knight: King of Cards (p.64-83; 20 pp):
   o https://yachtclubgames.com/shovel-knight-king-of-cards-instruction-manual/
 4p Joustus Instruction Manual (p.84-98; 15 pp):
   o https://yachtclubgames.com/joustus-instruction-manual/
 5 Shovel Knight Showdown (p.99-118; 20 pp):
   o https://yachtclubgames.com/shovel-knight-showdown-instruction-manual/
 amiibo (p.119-136; 18 pp):
   o https://yachtclubgames.com/sk-amiibo-manual/
 Support with FAQ (p.137-139; 3 pp):
   o https://yachtclubgames.com/about/#faq
=> I just converted all 9 webpages to PDFs via Web2PDF (and FAQ directly):
  * https://www.web2pdfconvert.com/
  -> Note that without payment there is a daily limit - about 3 webpages.
To make one big Instruction Manual for entire Treasure Trove via ghostscript (given in as "<one line!>"):
"gs -dNOPAUSE -sDEVICE=pdfwrite -sOUTPUTFILE=Shovel_Knight__Treasure_Trove__All_9p1_Instruction_Manuals__20140617_to_20191207__JMB.pdf -dBATCH Shovel_Knight_X__Treasure_Trove__Instruction_Manual__20191125.pdf Shovel_Knight_1__Shovel_of_Hope__Instruction_Manual__20140617.pdf Shovel_Knight_1__Shovel_of_Hope__locCoop_Instruction_Manual__20170424.pdf Shovel_Knight_2__Plague_of_Shadows__Instruction_Manual__20150826.pdf Shovel_Knight_3__Specter_of_Torment__Instruction_Manual__20170227.pdf Shovel_Knight_4__King_of_Cards__Instruction_Manual__20191125.pdf Shovel_Knight_4__King_of_Cards_Joustus_Instruction_Manual__20191206.pdf Shovel_Knight_5__Showdown__Instruction_Manual__20191207.pdf Shovel_Knight__amiibo_Instruction_Manual__20151130.pdf Shovel_Knight__Support_and_FAQ__20131009.pdf"

I asked the support (i.e. developers):
"I created a new Manual for `Shovel Knight: Treasure Trove' from your 9 web manuals and the support page -
 summing up to 139 pages and 6.2 MB:
   *
https://www.jmb-edu.de/pdfs/Shovel_Knight__Treasure_Trove__All_9p1_Instruction_Manuals__20140617_to_20191207__JMB.pdf
 Reason for this was that I spotted on GOG forum this thread:
   * https://www.gog.com/forum/shovel_knight/is_there_a_manual_pdf
 giving an old PDF out of 3 of your former Manuals summing up to 49 pages and 3.6 MB ...
 so I just created a new one and would give my link above in a new forum post there if this is legally OK,
 i.e. if you grant permission to translate your pages to PDF and provide an entire PDF Manual
 for your terrific game.
 Currently my new manal is not linked on my site and thus not visible to Google and others -
 and I will delete it directly if you so desire - and otherwise wait for an answer to link it and
 make a forum post.
 But I would be glad if I could provide it for those gamers who prefer a PDF manual -
 and would be willing to even include it to GOG offering as additional `Goody' if that pleases you."
and got the reply (on 08. Jan. 2021 23:10):
"So long as you are not profiting off of the material, it's fine. And provided you're or the use of the document
 is not used in a way that is pretending to be a representative of Yacht Club Games."
So my thanks to the developers to be able to provide the PDF to others!

Hope it may help - or be a joy for those accustomed to PDF manuals!