Clarify the proper 'make-mode' usage in the docs

[jdillard]

Subject: Clarify the proper 'make-mode' usage in the docs.

Feature or Bugfix

• Bugfix documentation

Purpose

• The fact that source and output directories need to come first isn't mentioned, which can lead to usage issues.

Relates

• Fixes the issue mentioned here: sphinx-build -M html -c . sets the config dir to be ./html #10968 (comment)

[picnixz]

Thank you!