Update API Reference docs and settings

Author: maryamziaa

.gitignore

@@ -52,6 +52,7 @@
 
 # Generated doc folders
 /docs/html
+/com.unity.ml-agents/Documentation~/html
 
 # Mac hidden files
 *.DS_Store

com.unity.ml-agents/Documentation~/API-Reference.md

@@ -4,7 +4,7 @@ Our developer-facing C# classes have been documented to be compatible with
 Doxygen for auto-generating HTML documentation.
 
 To generate the API reference, download Doxygen and run the following command
-within the `docs/` directory:
+within the `Documentation~/` directory:
 
 ```sh
 doxygen dox-ml-agents.conf

com.unity.ml-agents/Documentation~/dox-ml-agents.conf

@@ -783,7 +783,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../com.unity.ml-agents/Runtime/
+INPUT                  = ../Runtime/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses