diff --git a/src/formatitko/command.py b/src/formatitko/command.py
index 99ff04f..249e080 100644
--- a/src/formatitko/command.py
+++ b/src/formatitko/command.py
@@ -1,8 +1,9 @@
-from panflute import Div, Span, Para, Element
+from panflute import Span, Div, Element, Plain, Para
 
-# Import local files
-from .util import nullify, import_md
-from .context import Context
+from .util import inlinify
+
+class InlineError(Exception):
+	pass
 
 class Command:
 	pass
@@ -14,10 +15,10 @@ class InlineCommand(Span, Command):
 		try:
 			return Span(*content)
 		except TypeError:
-			if len(content) == 1 and isinstance(content[0], Para):
-				return Span(*content[0].content)
+			if inlinify(content):
+				return Span(inlinify(content))
 			else:
-				raise SyntaxError(f"The command {self.attributes['c']} returned multiple Paragraphs and must be executed using `::: {{c={self.attributes['c']}}}\\n:::`.")
+				raise InlineError(f"The command {self.attributes['c']} returned multiple Paragraphs and must be executed using `::: {{c={self.attributes['c']}}}\\n:::`.\n\n{content}")
 	pass
 
 class BlockCommand(Div, Command):
@@ -25,69 +26,3 @@ class BlockCommand(Div, Command):
 		return Div(*content)
 	pass
 
-# This function is called in trasform.py, defining a command which can be
-# called later using the function below
-def handle_command_define(e: Element, c: Context):
-	if "define" in e.attributes:
-		if not c.get_command(e.attributes["define"]):
-			c.set_command(e.attributes["define"], compile(e.text, '<string>', 'exec'))
-			return nullify(e)
-		else:
-			raise NameError(f"Command already defined: '{e.attributes['define']}'")
-	if "redefine" in e.attributes:
-		c.set_command(e.attributes["redefine"], compile(e.text, '<string>', 'exec'))
-		return nullify(e)
-	return e
-
-# This function executes commands and inline runnable code blocks (see
-# transform.py for their syntax). Context can be accessed using `ctx` and there
-# are four functions available to create output from these commands and the
-# element the command has been called on (including its .content) can be
-# accessed using `element`. Arguments can be passed down to the comand using
-# the element's attributes.
-#
-# print and println append text to a buffer which is then interpreted as
-# markdown with the current context.
-#
-# appendChild and appendChildren append panflute elements to a list which is
-# then transformed. A command which does nothing looks like this:
-# ```python {define=nop}
-# appendChildren(element.content)
-# ```
-#
-# These two types, appending and printing, cannot be mixed.
-
-def executeCommand(source, element: Element, ctx: Context) -> list[Element]:
-	mode = 'empty'
-	text = ""
-	content = []
-	def print(s: str=""):
-		nonlocal mode, text
-		if mode == 'elements':
-			raise SyntaxError("Cannot use `print` and `appendChild` in one command at the same time.")
-		mode = 'text'
-		text += str(s)
-
-	def println(s: str=""):
-		print(str(s)+"\n")
-
-	def appendChild(e: Element):
-		nonlocal mode, content
-		if mode == 'text':
-			raise SyntaxError("Cannot use `print` and `appendChild` in one command at the same time.")
-		mode = 'elements'
-		content.append(e)
-
-	def appendChildren(l: list[Element]):
-		for e in l:
-			appendChild(e)
-
-	import panflute as pf
-	exec(source)
-
-	if mode == 'text':
-		return import_md(text, standalone=False)
-	if mode == 'elements':
-		return content
-
-	return []
diff --git a/src/formatitko/command_env.py b/src/formatitko/command_env.py
new file mode 100644
index 0000000..15529ff
--- /dev/null
+++ b/src/formatitko/command_env.py
@@ -0,0 +1,7 @@
+import panflute as pf
+import formatitko.elements as fe
+from formatitko.util import import_md_list
+
+from formatitko.context import Context
+from formatitko.command import Command
+from panflute import Element
diff --git a/src/formatitko/command_util.py b/src/formatitko/command_util.py
new file mode 100644
index 0000000..d68815e
--- /dev/null
+++ b/src/formatitko/command_util.py
@@ -0,0 +1,37 @@
+from .context import Context, CommandCallable  # This is there because of a wild circular import dependency between many functions and classes
+from panflute import CodeBlock
+
+
+from . import command_env
+from .util import nullify
+
+def parse_command(code: str) -> CommandCallable:
+	code_lines = code.split("\n")
+	tabs = False
+	for line in code_lines:
+		if len(line) != 0 and line[0] == "\t":
+			tabs = True
+			break
+	indented_code_lines = []
+	for line in code_lines:
+		indented_code_lines.append(("\t" if tabs else "    ")+line)
+	code = "def command(element: Command, context: Context) -> list[Element]:\n"+"\n".join(indented_code_lines)
+	globals = command_env.__dict__
+	exec(code, globals)
+	return globals["command"]
+
+# This function is called in trasform.py, defining a command which can be
+# called later
+def handle_command_define(e: CodeBlock, c: Context):
+	command = parse_command(e.text)
+	if "define" in e.attributes:
+		if not c.get_command(e.attributes["define"]):
+			c.set_command(e.attributes["define"], command)
+			return nullify(e)
+		else:
+			raise NameError(f"Command already defined: '{e.attributes['define']}'")
+	if "redefine" in e.attributes:
+		c.set_command(e.attributes["redefine"], command)
+		return nullify(e)
+	return e
+
diff --git a/src/formatitko/context.py b/src/formatitko/context.py
index 24f98ee..96e112e 100644
--- a/src/formatitko/context.py
+++ b/src/formatitko/context.py
@@ -1,8 +1,14 @@
+from panflute import Doc, Element, Div
 
-from panflute import Doc, Div
+from typing import Union, Callable
+from types import ModuleType
 import os
 import warnings
 
+from .command import Command
+
+CommandCallable = Callable[[Command, 'Context'], list[Element]] # This is here because of a wild circular import dependency between many functions and classes
+
 # This class is used to keep state while transforming the document using
 # transform.py. For the context to be available to the html and TeX generators,
 # individual keys must be manually assigned to the individual elements. This is
@@ -15,7 +21,7 @@ import warnings
 # This class is basically an extension to panflute's doc, this is why metadata
 # is read directly from it.
 class Context:
-	def __init__(self, doc: Doc, path: str, parent: 'Context'=None, trusted: bool=True):
+	def __init__(self, doc: Doc, path: str, parent: Union['Context', None]=None, trusted: bool=True):
 		self.parent = parent
 		self._commands = {}
 		self.doc = doc
@@ -26,7 +32,7 @@ class Context:
 		if self.get_metadata("flags", immediate=True) is None:
 			self.set_metadata("flags", {})
 
-	def get_command(self, command: str):
+	def get_command(self, command: str) -> Union[CommandCallable, None]:
 		if command in self._commands:
 			return self._commands[command]
 		elif self.parent:
@@ -34,12 +40,18 @@ class Context:
 		else:
 			return None
 
-	def set_command(self, command: str, val):
+	def set_command(self, command: str, val: CommandCallable):
 		self._commands[command] = val
-	
+
 	def unset_command(self, command: str):
 		del self._commands[command]
 
+	def add_commands_from_module(self, module: ModuleType, module_name: str=""):
+		prefix = module_name+"." if module_name else ""
+		for name, func in module.__dict__.items():
+			if isinstance(func, CommandCallable):
+				self.set_command(prefix+name, func)
+
 	def is_flag_set(self, flag: str):
 		if self.get_metadata("flags."+flag):
 			if self.get_metadata("flags."+flag):
@@ -74,7 +86,7 @@ class Context:
 		for k in keys[:-1]:
 			meta = meta[k]
 		meta[keys[-1]] = value
-	
+
 	def unset_metadata(self, key: str):
 		meta = self.doc.metadata
 		keys = key.split(".")
@@ -91,3 +103,4 @@ class Group(Div):
 	def __init__(self, *args, metadata={}, **kwargs):
 		self.metadata = metadata
 		super().__init__(*args, **kwargs)
+
diff --git a/src/formatitko/elements.py b/src/formatitko/elements.py
new file mode 100644
index 0000000..25aea17
--- /dev/null
+++ b/src/formatitko/elements.py
@@ -0,0 +1,15 @@
+from panflute import Quoted
+
+
+from .command import Command, InlineCommand, BlockCommand
+from .context import Group
+from .whitespace import Whitespace, NBSP
+
+# This is a small extension to the Quoted panflute elements which allows to
+# have language-aware quotation marks.
+class FQuoted(Quoted):
+	def __init__(self, *args, **kwargs):
+		self.style = kwargs["style"]
+		del kwargs["style"]
+		super().__init__(*args, **kwargs)
+
diff --git a/src/formatitko/formatitko.py b/src/formatitko/formatitko.py
index 1d0d3ca..03dfe49 100755
--- a/src/formatitko/formatitko.py
+++ b/src/formatitko/formatitko.py
@@ -58,6 +58,7 @@ def main():
 		#open(args.output_html, "w").write(html(doc, katexClient, imageProcessor))
 		#open(args.output_tex, "w").write(tex(doc, imageProcessor))
 		HTMLGenerator(sys.stdout, katexClient, imageProcessor).generate(doc)
+		# OutputGenerator(sys.stdout).generate(doc)
 
 	if args.debug:
 		print(show(doc))
diff --git a/src/formatitko/html.py b/src/formatitko/html.py
index 28e408b..0403082 100644
--- a/src/formatitko/html.py
+++ b/src/formatitko/html.py
@@ -7,7 +7,7 @@ import os
 from typing import Union
 
 from .whitespace import NBSP
-from .transform import FQuoted
+from .elements import FQuoted
 from .katex import KatexClient
 from .util import inlinify
 from .context import Group
diff --git a/src/formatitko/latex_generator.py b/src/formatitko/latex_generator.py
index 92f9082..40ae889 100644
--- a/src/formatitko/latex_generator.py
+++ b/src/formatitko/latex_generator.py
@@ -5,7 +5,7 @@ from panflute import TableRow, TableCell, Caption, Doc
 from typing import Union
 
 from .whitespace import NBSP
-from .transform import FQuoted
+from .elements import FQuoted
 from .context import Group
 from .output_generator import OutputGenerator
 from .images import ImageProcessor
diff --git a/src/formatitko/output_generator.py b/src/formatitko/output_generator.py
index 7abdcd2..783e790 100644
--- a/src/formatitko/output_generator.py
+++ b/src/formatitko/output_generator.py
@@ -5,7 +5,7 @@ from panflute import TableRow, TableCell, Caption, Doc
 from typing import Union
 
 from .whitespace import NBSP
-from .transform import FQuoted
+from .elements import FQuoted
 from .context import Group
 
 import re
diff --git a/src/formatitko/tex.py b/src/formatitko/tex.py
index 5352fd3..23a2d62 100644
--- a/src/formatitko/tex.py
+++ b/src/formatitko/tex.py
@@ -3,7 +3,7 @@ import os
 from typing import Union
 
 from .whitespace import NBSP
-from .transform import FQuoted
+from .elements import FQuoted
 from .util import inlinify
 from .context import Group
 from .images import ImageProcessor
diff --git a/src/formatitko/transform.py b/src/formatitko/transform.py
index d422060..c96c6e6 100644
--- a/src/formatitko/transform.py
+++ b/src/formatitko/transform.py
@@ -1,21 +1,14 @@
-from panflute import Element, Div, Span, Quoted, Image, CodeBlock, Str, MetaInlines, MetaString, MetaBool
+from panflute import Element, Div, Span, Quoted, Image, CodeBlock, Str, MetaInlines, MetaString, MetaBool, RawBlock
 import re
+import os
 
 # Import local files
 from .whitespace import Whitespace, NBSP, bavlna
-from .command import Command, BlockCommand, InlineCommand, handle_command_define, executeCommand
 from .util import nullify, import_md
 from .context import Context, Group
-
-
-# This is a small extension to the Quoted panflute elements which allows to
-# have language-aware quotation marks.
-class FQuoted(Quoted):
-	def __init__(self, *args, **kwargs):
-		self.style = kwargs["style"]
-		del kwargs["style"]
-		super().__init__(*args, **kwargs)
-
+from .command import Command, BlockCommand, InlineCommand
+from .command_util import handle_command_define, parse_command
+from .elements import FQuoted
 
 # This is where tha magic happens. This function transforms a single element,
 # to transform the entire tree, panflute's walk should be used.
@@ -117,7 +110,8 @@ def transform(e: Element, c: Context) -> Element:
 	if isinstance(e, CodeBlock) and hasattr(e, "classes") and "python" in e.classes and "run" in e.classes:
 		if not c.trusted:
 			return nullify(e)
-		e = Div(*executeCommand(e.text, None, c))
+		command_output = parse_command(e.text)(BlockCommand(), c)
+		e = Div(*([] if command_output is None else command_output))
 		e = e.walk(transform, c)
 
 	# Command defines for calling using BlockCommand and InlineCommand. If
@@ -169,7 +163,8 @@ def transform(e: Element, c: Context) -> Element:
 	if isinstance(e, Command):
 		if not c.get_command(e.attributes["c"]):
 			raise NameError(f"Command not defined '{e.attributes['c']}'.")
-		e = e.replaceSelf(executeCommand(c.get_command(e.attributes["c"]), e, c))
+		command_output = c.get_command(e.attributes["c"])(e, c)
+		e = e.replaceSelf([] if command_output is None else command_output)
 		e = e.walk(transform, c)
 
 	return e
diff --git a/src/formatitko/util.py b/src/formatitko/util.py
index 676c1cc..3710c72 100644
--- a/src/formatitko/util.py
+++ b/src/formatitko/util.py
@@ -1,25 +1,38 @@
-from panflute import Element, Block, Inline, Null, Str, Doc, convert_text, Para, Plain
+from panflute import Element, Block, Inline, Null, Str, Doc, convert_text, Para, Plain, Span
 import re
+from typing import Union
 
 # It sometimes happens that an element contains a single paragraph or even a
 # single plaintext line. It can be sometimes useful to extract this single
 # paragraph, which is inline.
-def inlinify(e: Element) -> Element:
-	if len(e.content) == 1 and (isinstance(e.content[0], Para) or isinstance(e.content[0], Plain)):
-		return e.content[0].content
+def inlinify(e: Union[Element, list[Element]]) -> Union[Element, None]:
+	if isinstance(e, Element):
+		content = e.content
+	else:
+		content = e
+	if len(content) == 0:
+		return Str("")
+	if len(content) == 1 and (isinstance(content[0], Para) or isinstance(content[0], Plain)):
+		return Span(*content[0].content)
+	if len(content) == 1 and inlinify(content[0]) is not None:
+		return inlinify(content[0])
+	return None
 
 # In transform, inline elements cannot be replaced with Block ones and also
 # cannot be removed from the tree entirely, because that would mess up the
 # iteration process through the tree. We replace them with null elements
 # instead which never make it to the output.
-def nullify(e: Element):
+def nullify(e: Element) -> Union[Str, Null]:
 	if isinstance(e, Inline):
 		return Str("")
-	elif isinstance(e, Block):
+	else:
 		return Null()
 
 # A helper function to import markdown using panflute (which calls pandoc). If
 # we ever want to disable or enable some of panflute's markdown extensions,
 # this is the place to do it.
-def import_md(s: str, standalone: bool=True) -> Doc:
+def import_md(s: str, standalone: bool=True) -> Union[Doc, list[Element]]:
 	return convert_text(s, standalone=standalone, input_format="markdown-definition_lists-citations-latex_macros")
+
+def import_md_list(s: str) -> list[Element]:
+	return import_md(s, standalone=False)