Remove all mutators/accessors called only once in the code.

Avoid to have the API for options mixed with other code. This trigger a
number of fixes in the standard C headers that must be included.

<tao-utils.h> -> <tao-time.h> and <tao-utils.h>
<tao-threads.h> -> <tao-semaphores.h> and <tao-threads.h>