docs: make doxygen happy with new locations

Change @file entry on some headers due to duplicated files in the
include/ tree (real header + shim).
Adapt the doxygen configuration file to the new locations and remove
directories which are already included.

Signed-off-by: Anas Nashif <anas.nashif@intel.com>

include/debug/stack.h

@@ -1,5 +1,5 @@
 /**
- * @file stack.h
+ * @file debug/stack.h
  * Stack usage analysis helpers
  */
 

include/drivers/entropy.h

@@ -1,5 +1,5 @@
 /**
- * @file entropy.h
+ * @file drivers/entropy.h
  *
  * @brief Public APIs for the entropy driver.
  */

include/drivers/sensor.h

@@ -1,5 +1,5 @@
 /**
- * @file sensor.h
+ * @file drivers/sensor.h
  *
  * @brief Public APIs for the sensor driver.
  */