diff --git a/classes/base.lua b/classes/base.lua
index e91b2feec..7cd902029 100644
--- a/classes/base.lua
+++ b/classes/base.lua
@@ -575,9 +575,9 @@ function class:finish ()
   end
   SILE.typesetter:runHooks("pageend") -- normally run by the typesetter
   self:endPage()
-    if SILE.typesetter then
-      assert(SILE.typesetter:isQueueEmpty(), "queues not empty")
-    end
+  if SILE.typesetter then
+    assert(SILE.typesetter:isQueueEmpty(), "queues not empty")
+  end
   SILE.outputter:finish()
   self:runHooks("finish")
 end
diff --git a/core/makedeps.lua b/core/makedeps.lua
index 41718b6da..5e194821c 100644
--- a/core/makedeps.lua
+++ b/core/makedeps.lua
@@ -25,7 +25,7 @@ local makeDeps = {
   write = function (self)
     self:add_modules()
     if type(self.filename) ~= "string" then
-      self.filename = SILE.masterFilename .. ".d"
+      self.filename = pl.path.splitext(SILE.input.filenames[1]) .. ".d"
     end
     local depfile, err = io.open(self.filename, "w")
     if not depfile then return SU.error(err) end
diff --git a/core/sile.lua b/core/sile.lua
index eb9471610..377f73c14 100644
--- a/core/sile.lua
+++ b/core/sile.lua
@@ -291,7 +291,7 @@ function SILE.processString (doc, format, filename, options)
   -- a specific inputter to use, use it at the exclusion of all content type
   -- detection
   local inputter
-  if filename and pl.path.splitext(pl.path.normcase(filename)) == SILE.masterFilename and SILE.inputter then
+  if filename and pl.path.normcase(pl.path.normpath(filename)) == pl.path.normcase(SILE.input.filenames[1]) and SILE.inputter then
     inputter = SILE.inputter
   else
     format = format or detectFormat(doc, filename)
@@ -301,7 +301,7 @@ function SILE.processString (doc, format, filename, options)
     inputter = SILE.inputters[format](options)
     -- If we did content detection *and* this is the master file, save the
     -- inputter for posterity and postambles
-    if filename and pl.path.splitext(pl.path.normcase(filename)) == SILE.masterFilename then
+    if filename and pl.path.normcase(filename) == pl.path.normcase(SILE.input.filenames[1]) then
       SILE.inputter = inputter
     end
   end
@@ -315,17 +315,15 @@ function SILE.processFile (filename, format, options)
   local doc
   if filename == "-" then
     filename = "STDIN"
-    SILE.masterFilename = "STDIN"
     doc = io.stdin:read("*a")
   else
     -- Turn slashes around in the event we get passed a path from a Windows shell
     filename = filename:gsub("\\", "/")
     if not SILE.masterFilename then
-      -- Strip extension
-      SILE.masterFilename = string.match(filename, "(.+)%..-$") or filename
+      SILE.masterFilename = pl.path.splitext(pl.path.normpath(filename))
     end
-    if SILE.masterFilename and not SILE.masterDir then
-      SILE.masterDir = SILE.masterFilename:match("(.-)[^%/]+$")
+    if SILE.input.filenames[1] and not SILE.masterDir then
+      SILE.masterDir = pl.path.dirname(SILE.input.filenames[1])
     end
     if SILE.masterDir and SILE.masterDir:len() >= 1 then
       _G.extendSilePath(SILE.masterDir)
@@ -463,7 +461,7 @@ function SILE.finish ()
   end
   if SU.debugging("profile") then
     ProFi:stop()
-    ProFi:writeReport(SILE.masterFilename..'.profile.txt')
+    ProFi:writeReport(pl.path.splitext(SILE.input.filenames[1]) .. '.profile.txt')
   end
   if SU.debugging("versions") then
     SILE.shaper:debugVersions()
diff --git a/documentation/c10-classdesign.sil b/documentation/c10-classdesign.sil
index 6038fdf11..e658d0327 100644
--- a/documentation/c10-classdesign.sil
+++ b/documentation/c10-classdesign.sil
@@ -496,7 +496,7 @@ Here is a function to be called by the \code{finish} output routine:
 function package.writeToc (_)
   -- (Simplified from the actual implementation.)
   local tocdata = pl.pretty.write(SILE.scratch.tableofcontents)
-  local tocfile, err = io.open(SILE.masterFilename .. '.toc', "w")
+  local tocfile, err = io.open(pl.path.splitext(SILE.input.filenames[1]) .. '.toc', "w")
   if not tocfile then return SU.error(err) end
   tocfile:write("return " .. tocdata)
   tocfile:close()
diff --git a/outputters/base.lua b/outputters/base.lua
index b130f4b10..a5ce0aacd 100644
--- a/outputters/base.lua
+++ b/outputters/base.lua
@@ -38,8 +38,8 @@ function outputter:getOutputFilename ()
   local fname
   if SILE.outputFilename then
     fname = SILE.outputFilename
-  elseif SILE.masterFilename then
-    fname = SILE.masterFilename
+  elseif SILE.input.filenames[1] then
+    fname = pl.path.splitext(SILE.input.filenames[1])
     if self.extension then
       fname = fname .. "." .. self.extension
     end
diff --git a/packages/cropmarks/init.lua b/packages/cropmarks/init.lua
index f206a310d..59b6b8f71 100644
--- a/packages/cropmarks/init.lua
+++ b/packages/cropmarks/init.lua
@@ -64,7 +64,7 @@ end
 function package:registerCommands ()
 
   self:registerCommand("crop:header", function (_, _)
-    local info = SILE.masterFilename .. " - " .. self.class:date("%x %X") .. " -  " .. outcounter
+    local info = SILE.input.filenames[1] .. " - " .. self.class:date("%x %X") .. " -  " .. outcounter
     SILE.typesetter:typeset(info)
   end)
 
diff --git a/packages/tableofcontents/init.lua b/packages/tableofcontents/init.lua
index 0fb8bd667..9c74ef9d6 100644
--- a/packages/tableofcontents/init.lua
+++ b/packages/tableofcontents/init.lua
@@ -19,7 +19,7 @@ end
 
 function package.writeToc (_)
   local tocdata = pl.pretty.write(SILE.scratch.tableofcontents)
-  local tocfile, err = io.open(SILE.masterFilename .. '.toc', "w")
+  local tocfile, err = io.open(pl.path.splitext(SILE.input.filenames[1]) .. '.toc', "w")
   if not tocfile then return SU.error(err) end
   tocfile:write("return " .. tocdata)
   tocfile:close()
@@ -34,7 +34,7 @@ function package.readToc (_)
     -- already loaded
     return SILE.scratch._tableofcontents
   end
-  local tocfile, _ = io.open(SILE.masterFilename .. '.toc')
+  local tocfile, _ = io.open(pl.path.splitext(SILE.input.filenames[1]) .. '.toc')
   if not tocfile then
     return false -- No TOC yet
   end