* docs: remove unreferenced user guides
Drop docs/command-line.md, databases.md, java.md, unity-external-editor.md
and docs/media/debug.jpg. Nothing in the repository links to them.
Plugin, theme and README assets under docs/ stay.
* docs: keep only plugin docs under docs/
Remove docs/themes.md and docs/data-directories.md. Move the upstream
Atom One source revisions into THIRD_PARTY_LICENSES.md, drop the links
to the removed page, and move the README's WeChat QR code to
.github/assets/.
* docs: move plugin docs next to plugins/README.md
docs/plugins/themes.md and indexing.md move to plugins/. Update the
theme doc generator, its test, the plugin template, AGENTS.md and every
link to the new paths.