'He said that Mary had done that.'

Often, you get tense agreement between a matrix and subordinate clause:

So 'he said that she had done that' could be reflecting this tense
agreement rather than the tense/aspect qualities of Mary's action.
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Johanna Rubba   Assistant Professor, Linguistics
English Department, California Polytechnic State University
One Grand Avenue  • San Luis Obispo, CA 93407
Tel. (805)-756-2184  •  Fax: (805)-756-6374 • Dept. Phone.  756-259
• E-mail: [log in to unmask] •  Home page: http://www.cla.calpoly.edu/~jrubba
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