MB-6141: Update doxygen config with correct source directories

Change-Id: I2bdbb4b769833daef3b73adcdfdd08598465ee2d
Reviewed-on: http://review.couchbase.org/20209
Reviewed-by: Chiyoung Seo <chiyoung.seo@gmail.com>
Tested-by: Chiyoung Seo <chiyoung.seo@gmail.com>

Doxyfile

@@ -574,7 +574,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  =
+INPUT                  = src/ src/atomic src/blackhole-kvstore src/couch-kvstore
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is