When to stop marking up your text

Use markup to express:

1. a canonical citation scheme. Readers must be able to cite your edition.
2. editorial status of text contents. Readers need to know what you could read and what you had to make up (supply, correct, emend...)
3. manual disambiguation of material that would otherwise be automatically analyzed.

That's it.

Any other analytical information can be expressed outside of your edition. (Remember the preliminary rule: editing and reading texts are different interpretive activities. ) Relating a citable passage of your text to an analysis requires nothing more than pairing a text citation with a citation of your analysis.