The %. keyword instructs Twelf to stop reading input in the current file. It is most useful in emacs mode to check some prefix of a file that you are currently working on.
The following example shows a simple Twelf declaration at top, and the text below it in green shows the response from Twelf. Notice that the last three lines are not considered by Twelf, because it stops reading input when it reaches the %. keyword.
nat : type. %. This line will not be checked. Neither will anything else that gets put after the %. %total T (pretendlemma T _ _).
Twelf 1.7.1+ (r1896, built 05/05/15 at 12:56:43 on yazoo.plparty.org)
nat : type.%% OK %%