diff --git a/src/resources/filters/ast/customnodes.lua b/src/resources/filters/ast/customnodes.lua
index ca61ebc39b9..ecda0ccb24a 100644
--- a/src/resources/filters/ast/customnodes.lua
+++ b/src/resources/filters/ast/customnodes.lua
@@ -336,16 +336,21 @@ _quarto.ast = {
           return
         end
         local node = node_accessor(table)
-        local t = pandoc.utils.type(value)
-        quarto_assert(t ~= 'Div' and t ~= 'Span', "")
+        local valtype = pandoc.utils.type(value)
+        quarto_assert(valtype ~= 'Div' and valtype ~= 'Span', "")
         if index > #node.content then
           _quarto.ast.grow_scaffold(node, index)
         end
-        local pt = pandoc.utils.type(value)
-        if pt == "Block" or pt == "Inline" then
-          node.content[index].content = {value}
+        local inner_node = node.content[index]
+        local innertype = pandoc.utils.type(inner_node)
+        if innertype == 'Block' then
+          inner_node.content = quarto.utils.as_blocks(value)
+        elseif innertype == 'Inline' then
+          inner_node.content = quarto.utils.as_inlines(value)
         else
-          node.content[index].content = value
+          warn(debug.traceback(
+                 'Cannot find the right content type for value ' .. valtype))
+          inner_node.content = value
         end
       end
     }
@@ -416,13 +421,15 @@ _quarto.ast = {
       -- luacov: enable
     end
 
-    local forwarder = { }
+    local forwarder
     if tisarray(handler.slots) then
+      forwarder = pandoc.List{}
       for i, slot in ipairs(handler.slots) do
         forwarder[slot] = i
       end
-    else
-      forwarder = handler.slots
+    elseif handler.slots ~= nil then
+      warn('Expected `slots` to be either an array or nil, got ' ..
+           tostring(handler.slots))
     end
 
     quarto[handler.ast_name] = function(params)
diff --git a/src/resources/filters/crossref/equations.lua b/src/resources/filters/crossref/equations.lua
index f8a12e64f28..0ecb0e430b7 100644
--- a/src/resources/filters/crossref/equations.lua
+++ b/src/resources/filters/crossref/equations.lua
@@ -20,7 +20,7 @@ function process_equations(blockEl)
   end
 
   local mathInlines = nil
-  local targetInlines = pandoc.List()
+  local targetInlines = pandoc.Inlines{}
 
   for i, el in ipairs(inlines) do
 
diff --git a/src/resources/filters/crossref/index.lua b/src/resources/filters/crossref/index.lua
index 16ad656d1cc..68daa1ede38 100644
--- a/src/resources/filters/crossref/index.lua
+++ b/src/resources/filters/crossref/index.lua
@@ -65,9 +65,9 @@ end
 -- add an entry to the index
 function indexAddEntry(label, parent, order, caption, appendix)
   if caption ~= nil then
-    caption = pandoc.List(caption)
+    caption = quarto.utils.as_blocks(caption)
   else
-    caption = pandoc.List({})
+    caption = pandoc.Blocks({})
   end
   crossref.index.entries[label] = {
     parent = parent,
diff --git a/src/resources/filters/crossref/preprocess.lua b/src/resources/filters/crossref/preprocess.lua
index 1b995b78a6c..6a7c113fe2d 100644
--- a/src/resources/filters/crossref/preprocess.lua
+++ b/src/resources/filters/crossref/preprocess.lua
@@ -7,7 +7,7 @@ function crossref_mark_subfloats()
   return {
     traverse = "topdown",
     FloatRefTarget = function(float)
-      float.content = _quarto.ast.walk(float.content, {
+      float.content = _quarto.ast.walk(float.content or pandoc.Blocks{}, {
         FloatRefTarget = function(subfloat)
           float.has_subfloats = true
           crossref.subfloats[subfloat.identifier] = {
diff --git a/src/resources/filters/customnodes/callout.lua b/src/resources/filters/customnodes/callout.lua
index 8a9f4c17dee..929c9c5cb8a 100644
--- a/src/resources/filters/customnodes/callout.lua
+++ b/src/resources/filters/customnodes/callout.lua
@@ -264,7 +264,8 @@ function _callout_main()
       return _quarto.format.typst.function_call("callout", { 
         { "body", _quarto.format.typst.as_typst_content(callout.content) },
         { "title", _quarto.format.typst.as_typst_content(
-          callout.title or pandoc.Plain(_quarto.modules.callouts.displayName(callout.type))
+          (not quarto.utils.is_empty_node(callout.title) and callout.title) or
+          pandoc.Plain(_quarto.modules.callouts.displayName(callout.type))
         )},
         { "background_color", pandoc.RawInline("typst", background_color) },
         { "icon_color", pandoc.RawInline("typst", icon_color) },
@@ -406,4 +407,4 @@ function crossref_callouts()
       return callout
     end
   }
-end
\ No newline at end of file
+end
diff --git a/src/resources/filters/customnodes/content-hidden.lua b/src/resources/filters/customnodes/content-hidden.lua
index f27af5a5418..9117085009a 100644
--- a/src/resources/filters/customnodes/content-hidden.lua
+++ b/src/resources/filters/customnodes/content-hidden.lua
@@ -105,7 +105,8 @@ local _content_hidden_meta = nil
 function content_hidden_meta(meta)
   -- return {
   --   Meta = function(meta)
-  _content_hidden_meta = meta
+  -- The call to `pandoc.Meta` ensures that we hold a copy.
+  _content_hidden_meta = pandoc.Meta(meta)
   --   end
   -- }
 end
diff --git a/src/resources/filters/customnodes/floatreftarget.lua b/src/resources/filters/customnodes/floatreftarget.lua
index 03c7d35cc0d..9f75512fc0a 100644
--- a/src/resources/filters/customnodes/floatreftarget.lua
+++ b/src/resources/filters/customnodes/floatreftarget.lua
@@ -767,7 +767,7 @@ function float_reftarget_render_html_figure(float)
   local float_content = pandoc.Div(_quarto.ast.walk(float.content, {
     -- strip image captions
     Image = function(image)
-      image.caption = {}
+      image.caption = pandoc.Inlines{}
       return image
     end
   }) or pandoc.Div({})) -- this should never happen but the lua analyzer doesn't know it
@@ -1098,4 +1098,4 @@ end, function(float)
   return pandoc.Para({im})
 end)
 
-global_table_guid_id = 0
\ No newline at end of file
+global_table_guid_id = 0
diff --git a/src/resources/filters/customnodes/shortcodes.lua b/src/resources/filters/customnodes/shortcodes.lua
index ffb5cc1c7a2..32ad1128e69 100644
--- a/src/resources/filters/customnodes/shortcodes.lua
+++ b/src/resources/filters/customnodes/shortcodes.lua
@@ -11,7 +11,7 @@ _quarto.ast.add_handler({
   kind = "Inline",
 
   parse = function(span)
-    local inner_content = pandoc.List({})
+    local inner_content = pandoc.Inlines({})
 
     span.content = span.content:filter(function(el)
       return el.t == "Span"
@@ -78,9 +78,9 @@ _quarto.ast.add_handler({
     end
 
     local node = _quarto.ast.create_custom_node_scaffold("Shortcode", "Inline")
-    node.content = inner_content:map(function(el) 
-      return pandoc.Span({el}) 
-    end)
+    node.content = pandoc.Inlines(inner_content:map(function(el)
+      return pandoc.Span({el})
+    end))
     local tbl = {
       __quarto_custom_node = node,
       name = name,
diff --git a/src/resources/filters/layout/html.lua b/src/resources/filters/layout/html.lua
index dc387110211..317cd855656 100644
--- a/src/resources/filters/layout/html.lua
+++ b/src/resources/filters/layout/html.lua
@@ -190,7 +190,7 @@ function renderHtmlFigure(el, render)
   end)
 
   -- remove identifier (it is now on the div)
-  el.identifier = ""
+  el.attr.identifier = ""
   
   if not figureDiv.classes:find_if(function(str) return str:match("quarto%-figure%-.+") end) then
     -- apply standalone figure css if not already set
diff --git a/src/resources/filters/layout/lightbox.lua b/src/resources/filters/layout/lightbox.lua
index 15203c120fd..d2569bd68d5 100644
--- a/src/resources/filters/layout/lightbox.lua
+++ b/src/resources/filters/layout/lightbox.lua
@@ -176,10 +176,11 @@ function lightbox()
     return {{
       traverse = "topdown",
 
-      Meta = function(meta) 
+      Meta = function(meta)
         -- Set auto lightbox mode, if need be
         auto = lightbox_module.automatic(meta) == true
-      end, 
+        imgCount = 0
+      end,
       -- Find images that are already within links
       -- we'll use this to filter out these images if
       -- the most is auto
diff --git a/src/resources/filters/layout/typst.lua b/src/resources/filters/layout/typst.lua
index 4c875f9b4fa..83fdcc3e2be 100644
--- a/src/resources/filters/layout/typst.lua
+++ b/src/resources/filters/layout/typst.lua
@@ -11,7 +11,7 @@ function make_typst_figure(tbl)
   local identifier = tbl.identifier
   local separator = tbl.separator
 
-  if (not caption or #caption.content == 0) and tbl.separator == nil then
+  if quarto.utils.is_empty_node(caption) and tbl.separator == nil then
     separator = ""
   end
 
diff --git a/src/resources/filters/normalize/draft.lua b/src/resources/filters/normalize/draft.lua
index 7b9c718a18d..d3f043e6438 100644
--- a/src/resources/filters/normalize/draft.lua
+++ b/src/resources/filters/normalize/draft.lua
@@ -23,17 +23,17 @@ function normalize_draft()
       end
       is_draft = meta[kDraft] == true or tcontains(drafts, quarto.doc.input_file);     
     end,
-    Pandoc = function(pandoc) 
+    Pandoc = function(doc)
       if _quarto.format.isHtmlOutput() and not _quarto.format.isHtmlSlideOutput() then
         if is_draft and draft_mode == kDraftModeGone then
-          pandoc.blocks = {}
+          doc.blocks = pandoc.Blocks{}
           quarto.doc.includeText("in-header", '<meta name="quarto:status" content="' .. kDraftStatusRemove .. '">')
-          return pandoc
+          return doc
         elseif is_draft and draft_mode ~= kDraftModeGone then
           quarto.doc.includeText("in-header", '<meta name="quarto:status" content="' .. kDraftStatusDraft .. '">')
-          return pandoc
+          return doc
         end
       end
     end
   }
-end
\ No newline at end of file
+end
diff --git a/src/resources/filters/normalize/flags.lua b/src/resources/filters/normalize/flags.lua
index 8815da0a2fa..d695d39b452 100644
--- a/src/resources/filters/normalize/flags.lua
+++ b/src/resources/filters/normalize/flags.lua
@@ -107,8 +107,7 @@ function compute_flags()
         -- FIXME: are we actually triggering this with FloatRefTargets?
         -- table captions
         local kTblCap = "tbl-cap"
-        local tblCap = extractTblCapAttrib(node,kTblCap)
-        if hasTableRef(node) or tblCap then
+        if hasTableRef(node) or node.attr.attributes[kTblCap] then
           flags.has_table_captions = true
         end
 
diff --git a/src/resources/filters/quarto-init/metainit.lua b/src/resources/filters/quarto-init/metainit.lua
index 9c3a22407db..9b63df41219 100644
--- a/src/resources/filters/quarto-init/metainit.lua
+++ b/src/resources/filters/quarto-init/metainit.lua
@@ -8,6 +8,7 @@ function quarto_meta_init()
       read_includes(meta)
       init_crossref_options(meta)
       initialize_custom_crossref_categories(meta)
+      return meta
     end
   }
-end
\ No newline at end of file
+end
diff --git a/src/resources/filters/quarto-post/foldcode.lua b/src/resources/filters/quarto-post/foldcode.lua
index c5884a3da57..ab68552c298 100644
--- a/src/resources/filters/quarto-post/foldcode.lua
+++ b/src/resources/filters/quarto-post/foldcode.lua
@@ -65,7 +65,7 @@ function fold_code_and_lift_codeblocks()
       local prev_annotated_code_block_scaffold = nil
       local prev_annotated_code_block = nil
       -- ok to lift codeblocks
-      float.content = _quarto.ast.walk(float.content, {
+      float.content = _quarto.ast.walk(float.content or pandoc.Blocks{}, {
         traverse = "topdown",
         DecoratedCodeBlock = function(block)
           -- defer the folding of code blocks to the DecoratedCodeBlock renderer
diff --git a/src/resources/filters/quarto-post/typst.lua b/src/resources/filters/quarto-post/typst.lua
index 4a2e7f8d6f5..8ebd9c87596 100644
--- a/src/resources/filters/quarto-post/typst.lua
+++ b/src/resources/filters/quarto-post/typst.lua
@@ -19,7 +19,9 @@ function render_typst()
   return {
     {
       Meta = function(m)
-        m["toc-depth"] = PANDOC_WRITER_OPTIONS["toc_depth"]
+        -- This should be a number, but we must represent it as a string,
+        -- as numbers are disallowed as metadata values.
+        m["toc-depth"] = tostring(PANDOC_WRITER_OPTIONS["toc_depth"])
         m["toc-indent"] = option("toc-indent")
         if m["number-depth"] then
           number_depth = tonumber(pandoc.utils.stringify(m["number-depth"]))
@@ -138,7 +140,7 @@ function render_typst_fixups()
       end
 
       img.attributes["fig-align"] = nil
-      return pandoc.Inlines({
+      return pandoc.Plain({
         pandoc.RawInline("typst", "#align(" .. align .. ")["),
         img,
         pandoc.RawInline("typst", "]"),
diff --git a/src/resources/filters/quarto-pre/code-annotation.lua b/src/resources/filters/quarto-pre/code-annotation.lua
index 4fa26cf24a6..077a10077e6 100644
--- a/src/resources/filters/quarto-pre/code-annotation.lua
+++ b/src/resources/filters/quarto-pre/code-annotation.lua
@@ -310,7 +310,7 @@ function code_annotations()
       -- if code annotations is false, then shut it down
       if codeAnnotations ~= false then
 
-        local outputs = pandoc.List()
+        local outputs = pandoc.Blocks{}
 
         -- annotations[annotation-number] = {list of line numbers}
         local pendingAnnotations = nil
diff --git a/src/resources/filters/quarto-pre/output-location.lua b/src/resources/filters/quarto-pre/output-location.lua
index eebe8bc2121..c50d388248a 100644
--- a/src/resources/filters/quarto-pre/output-location.lua
+++ b/src/resources/filters/quarto-pre/output-location.lua
@@ -71,7 +71,7 @@ function output_location()
   if _quarto.format.isRevealJsOutput() then
     return {
       Blocks = function(blocks)
-        local newBlocks = pandoc.List()
+        local newBlocks = pandoc.Blocks{}
         for _,block in pairs(blocks) do
           local outputLoc = collectCellOutputLocation(block)
           if outputLoc then
diff --git a/src/resources/filters/quarto-pre/parsefiguredivs.lua b/src/resources/filters/quarto-pre/parsefiguredivs.lua
index ca075b0a5a9..868643cd308 100644
--- a/src/resources/filters/quarto-pre/parsefiguredivs.lua
+++ b/src/resources/filters/quarto-pre/parsefiguredivs.lua
@@ -236,7 +236,7 @@ function parse_floatreftargets()
     end
     local caption = refCaptionFromDiv(div)
     if caption ~= nil then
-      div.content:remove(#div.content)
+      div.content:remove()  -- drop the last element
     elseif div.attributes[caption_attr_key] ~= nil then
       caption = pandoc.Plain(string_to_quarto_ast_inlines(div.attributes[caption_attr_key]))
       div.attributes[caption_attr_key] = nil
@@ -246,10 +246,10 @@ function parse_floatreftargets()
       local found_caption = false
       content = _quarto.ast.walk(content, {
         Table = function(table)
-          if table.caption.long ~= nil then
+          -- check if caption is non-empty
+          if table.caption.long and next(table.caption.long) then
             found_caption = true
             caption = table.caption.long[1] -- what if there's more than one entry here?
-            table.caption.long = nil
             return table
           end
         end
@@ -458,7 +458,7 @@ function parse_floatreftargets()
               fig_attr.classes:insert(v)
             end
           end
-          image.caption = {}
+          image.caption = pandoc.Inlines{}
           return image
         end
       }) or fig.content[1] -- this shouldn't be needed but the lua analyzer doesn't know it
@@ -494,7 +494,7 @@ function parse_floatreftargets()
       end
       
       -- we've parsed the caption, so we can remove it from the table
-      el.caption.long = pandoc.List({})
+      el.caption.long = pandoc.Blocks({})
 
       if label == "" then
         return nil
@@ -602,7 +602,7 @@ function parse_floatreftargets()
         if img.identifier == "" then
           local caption = img.caption
           if #caption > 0 then
-            img.caption = nil
+            img.caption = pandoc.Inlines{}
             return pandoc.Figure(link, { long = { caption } })
           else
             return nil
@@ -819,4 +819,4 @@ function forward_cell_subcaps()
       return div
     end
   }
-end
\ No newline at end of file
+end
diff --git a/src/resources/filters/quarto-pre/table-captions.lua b/src/resources/filters/quarto-pre/table-captions.lua
index ede527f83e0..67a3917f75a 100644
--- a/src/resources/filters/quarto-pre/table-captions.lua
+++ b/src/resources/filters/quarto-pre/table-captions.lua
@@ -140,7 +140,7 @@ function applyTableCaptions(el, tblCaptions, tblLabels)
           cap:insert(pandoc.Str("{#" .. tblLabels[idx] .. "}"))
         end
         idx = idx + 1
-        el.caption.long = pandoc.Plain(cap)
+        el.caption.long = pandoc.Blocks{pandoc.Plain(cap)}
         return el
       end
     end,
@@ -231,7 +231,7 @@ function extractTblCapAttrib(el, name, subcap)
     else
       value = pandoc.List({ value })
     end
-    el.attr.attributes[name] = nil
+    -- el.attr.attributes[name] = nil
     return value
   end
   return nil
diff --git a/src/resources/filters/quarto-pre/table-rawhtml.lua b/src/resources/filters/quarto-pre/table-rawhtml.lua
index 41708cd51b0..e36e946c31b 100644
--- a/src/resources/filters/quarto-pre/table-rawhtml.lua
+++ b/src/resources/filters/quarto-pre/table-rawhtml.lua
@@ -14,23 +14,32 @@ function table_merge_raw_html()
 
   return {
     Blocks = function(blocks)
-      local pendingRaw = pandoc.List()
-      local merged = pandoc.List()
-      for i,el in ipairs(blocks) do
-        if _quarto.format.isRawHtml(el) and el.text:find(patterns.html_table_tag_name) then
-          pendingRaw:insert(el.text)
+      local pending_raw = pandoc.List()
+      local next_element_idx = 1
+      for _, el in ipairs(blocks) do
+        if _quarto.format.isRawHtml(el) and
+           el.text:find(patterns.html_table_tag_name) then
+          pending_raw:insert(el.text)
         else
-          if #pendingRaw > 0 then
-            merged:insert(pandoc.RawBlock("html", table.concat(pendingRaw, "\n")))
-            pendingRaw = pandoc.List()
+          if next(pending_raw) then
+            blocks[next_element_idx] =
+              pandoc.RawBlock("html", table.concat(pending_raw, "\n"))
+            pending_raw = pandoc.List()
+            next_element_idx = next_element_idx + 1
           end
-          merged:insert(el)
+          blocks[next_element_idx] = el
+          next_element_idx = next_element_idx + 1
         end
       end
-      if #pendingRaw > 0 then
-        merged:insert(pandoc.RawBlock("html", table.concat(pendingRaw, "\n")))
+      if #pending_raw > 0 then
+        blocks[next_element_idx] =
+          pandoc.RawBlock("html", table.concat(pending_raw, "\n"))
+        next_element_idx = next_element_idx + 1
       end
-      return merged
+      for i = next_element_idx, #blocks do
+        blocks[i] = nil
+      end
+      return blocks
     end
   }
 end
@@ -54,4 +63,4 @@ function table_respecify_gt_css()
       return el
     end
   }
-end
\ No newline at end of file
+end
diff --git a/src/resources/pandoc/datadir/init.lua b/src/resources/pandoc/datadir/init.lua
index 1dc45ed14b4..4c7f1eecac5 100644
--- a/src/resources/pandoc/datadir/init.lua
+++ b/src/resources/pandoc/datadir/init.lua
@@ -1546,9 +1546,9 @@ local function processTextDependency(dependency, meta)
    local textLoc = rawText.location
 
    if meta[textLoc] == nil then
-      meta[textLoc] = {}
+      meta[textLoc] = pandoc.List{}
    end
-   table.insert(meta[textLoc], pandoc.RawBlock(FORMAT, rawText.text))
+   meta[textLoc]:insert(pandoc.Blocks{pandoc.RawBlock(FORMAT, rawText.text)})
  end
 
  -- make the usePackage statement
@@ -1568,9 +1568,9 @@ local function usePackage(package, option)
    
    local headerLoc = resolveLocation(kInHeader)
    if meta[headerLoc] == nil then
-      meta[headerLoc] = {}
+      meta[headerLoc] = pandoc.List{}
    end
-   table.insert(meta[headerLoc], usePackage(rawPackage.package, rawPackage.options))
+   meta[headerLoc]:insert(usePackage(rawPackage.package, rawPackage.options))
  end
  
  
@@ -1584,28 +1584,28 @@ local function processDependencies(meta)
    -- holds a list of hashes for dependencies that
    -- have been processed. Process each dependency
    -- only once
-   local injectedText = {}
-   local injectedFile = {}
-   local injectedPackage = {}
+   local injectedText = pandoc.List{}
+   local injectedFile = pandoc.List{}
+   local injectedPackage = pandoc.List{}
 
   -- each line was written as a dependency.
   -- process them and contribute the appropriate headers
-  for line in io.lines(dependenciesFile) do 
+  for line in io.lines(dependenciesFile) do
     local dependency = json.decode(line)
     if dependency.type == 'text' then
       if not utils.table.contains(injectedText, dependency.content) then
          processTextDependency(dependency, meta)
-         injectedText[#injectedText + 1] = dependency.content   
+         injectedText:insert(dependency.content)
       end
     elseif dependency.type == "file" then
       if not utils.table.contains(injectedFile, dependency.content.path) then
          processFileDependency(dependency, meta)
-         injectedFile[#injectedFile + 1] = dependency.content.path
+         injectedFile:insert(dependency.content.path)
       end
     elseif dependency.type == "usepackage" then
       if not utils.table.contains(injectedPackage, dependency.content.package) then
          processUsePackageDependency(dependency, meta)
-         injectedPackage[#injectedPackage + 1] = dependency.content.package
+         injectedPackage:insert(dependency.content.package)
       end
     end
   end