The [Notebook App] uses Tcl as a markup language. This is certainly an easy way of storing and retrieving information, but how is it regarded considering cleanliness of coding? Is it considered bad practice?

Well, I have always found markup languages, in general, to be obtuse if not
actually hostile to use.

Some people prefer the verbosity and complexity of [TeX] related 
markup.  Some are satisfied with [HTML].  Some want some variation of
[SGML]/[XML] = there is one variant [[whose name escapes me - perhaps someone
will replace this parenthetical remark with its name]] used in [Linux]
documentation.

But SGML based markup is pretty wordy, if not obtuse when trying to do
various combinations.

In the Tcl man page world, the original docs were formatted with *roff
markup.  The reason for this was that the reference pages were installed
in the same hierarchy tree as other system documentation, allowing one
to use the man command to read the docs.

Later, when Windows was supported, doc was provided on that platform in
some kind of help file format.

Extension writers tended to use the *roff for most docs, though a few
(including [bwidget]) distributed their documentation in html.

A few efforts have occurred over the years to use something more
''cross platform''.  For instance, see the [tmml] for one effort to
use an xml like format for tcl man pages.

Then, as a part of the [tcllib] effort, the [doctools] module was created
so that tcllib module documentation could be more easily created.  A
developer using this notation can generate documentation files in a
variety of formats.

I believe that [[someone '''PLEASE''' replace this comment with the
appropriate reference!]] even tried the tcl commands as markup approach
as well.  Perhaps check this page's category list to see if you can
turn up something.
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[Category Documentation]