diff --git a/docs/source/dev/theory.rst b/docs/source/dev/theory.rst
index 23bc8f2..3470f64 100644
--- a/docs/source/dev/theory.rst
+++ b/docs/source/dev/theory.rst
@@ -4,19 +4,20 @@ Theory of Operation
 Execution Flow When Producing "doc" Output
 ------------------------------------------
 
-#. The command line argv is read in `__main__.main()`, 
-   which calls `commands.convert()`
-#. `commands.convert()` reads the input with `docparser.doc_parser_visitor()`,
-   which uses the `parsimonious` library to parse the input into an abstract
+#. The command line argv is read in :py:func:`ptulsconv.__main__.main()`, 
+   which calls :py:func:`ptulsconv.commands.convert()`
+#. :func:`ptulsconv.commands.convert()` reads the input with 
+   :func:`ptuslconv.docparser.doc_parser_visitor()`,
+   which uses the ``parsimonious`` library to parse the input into an abstract
    syntax tree, which the parser visitor uses to convert into a 
-   `docparser.doc_entity.SessionDescriptor`, which structures all of the data
-   in the session output.
+   :class:`ptulsconv.docparser.doc_entity.SessionDescriptor`, 
+   which structures all of the data in the session output.
 #. The next action based on the output format. In the 
    case of the "doc" output format, it runs some validations
-   on the input, and calls `commands.generate_documents()`.
-#. `commands.generate_documents()` creates the output folder, creates the
-   Continuity report with `pdf.continuity.output_continuity()` (this document 
+   on the input, and calls :func:`ptulsconv.commands.generate_documents()`.
+#. :func:`ptulsconv.commands.generate_documents()` creates the output folder, creates the
+   Continuity report with :func:`ptulsconv.pdf.continuity.output_continuity()` (this document 
    requires some special-casing), and at the tail calls...
-#. `commands.create_adr_reports()`, which creates folders for 
+#. :func:`ptulsconv.commands.create_adr_reports()`, which creates folders for 
 
 (FIXME finish this)
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