diff --git a/build-agda-html.rb b/build-agda-html.rb
index 54c37dc..e6582d0 100644
--- a/build-agda-html.rb
+++ b/build-agda-html.rb
@@ -1,8 +1,33 @@
 require "json"
 require "set"
+require "optparse"
 
-code_paths = Dir.glob("code/*").to_set
-code_paths += JSON.parse(File.read("data/submodules.json")).keys
+# For target_dir, use absolute paths because when invoking Agda, we'll be
+# using chdir.
+root_path = "code"
+target_dir = File.expand_path "code"
+data_file = "data/submodules.json"
+OptionParser.new do |opts|
+  opts.banner = "Usage: build-agda-html.rb [options]"
+
+  opts.on("--root-path=PATH", "Search for Agda project folders in the given location") do |f|
+    root_path = f
+  end
+  opts.on("--target-dir=PATH", "Generate HTML files into the given directory") do |f|
+    target_dir = File.expand_path f
+  end
+  opts.on("--data-file=FILE", "Specify the submodules.json that encodes nested submodule structure") do |f|
+    data_file = f
+  end
+end.parse!
+files = ARGV
+
+code_paths = Dir.entries(root_path).select do |f|
+  File.directory?(File.join(root_path, f)) and f != '.' and f != '..'
+end.to_set
+code_paths += JSON.parse(File.read(data_file)).keys if File.exists? data_file
+# Extending code_paths from submodules.json means that nested Agda modules
+# have their root dir correctly set.
 
 max_path = ->(path) {
   code_paths.max_by do |code_path|
@@ -17,7 +42,7 @@ max_path = ->(path) {
 }
 
 files_for_paths = {}
-Dir.glob("code/**/*.agda") do |agda_file|
+Dir.glob("**/*.agda", base: root_path) do |agda_file|
   best_path = max_path.call(agda_file)
   files_for_path = files_for_paths.fetch(best_path) do
     files_for_paths[best_path] = []
@@ -28,10 +53,13 @@ end
 
 original_wd = Dir.getwd
 files_for_paths.each do |path, files|
-  Dir.chdir(File.join [original_wd, path])
+  Dir.chdir(original_wd)
+  Dir.chdir(File.join(root_path, path))
+  html_dir = File.join [target_dir, path, "html"]
   files.each do |file|
-    puts "Invoking 'agda' on file: #{File.join [Dir.getwd, file]}"
-    `#{ARGV[0]} --local-interfaces #{file} --html --html-dir=html`
+    command = "#{ARGV[0]} --local-interfaces #{file} --html --html-dir=#{html_dir}"
+    puts command
+    `#{command}`
 
     # Allow some programs to fail (e.g., IO.agda in SPA without --guardedness)
     # fail unless $? == 0