Without this patch, i'm seeing sphinx-build emit:

 [...]doc/man1/notmuch-emacs-mua.rst:: WARNING: document isn't included in any toctree
---
 doc/index.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/doc/index.rst b/doc/index.rst
index 3f0e6e6..344606d 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -14,6 +14,7 @@ Contents:
    man1/notmuch-count
    man1/notmuch-dump
    notmuch-emacs
+   man1/notmuch-emacs-mua
    man5/notmuch-hooks
    man1/notmuch-insert
    man1/notmuch-new
-- 
2.8.1