Thanks for your work on this!

``dir/package/module.cover`` → :file:`{dir}/{package}/{module}.cover`

'``>>>>>>``' looks wrong.

``os.pathsep``: You can use :data:`os.pathsep` to get a link, I think.

+.. method:: CoverageResults.update(other)
FTR, there is a new way for doing such things: You can nest method directives in a class directive block.  See gettext.rst for an example.  Your patch needn’t change that now, not all docs have been updated, so it’s best to do as you did and follow the style of the rest of the file.  I propose to change it after your patch is committed.

+..
Stray dots at the end of the file.

The doc uses one or two spaces inconsistently.  I don’t know if it’s worth changing.