update git ignore and ignore warnings to make git and build perfectly clean

Author: JohnMoehrke

.gitignore

@@ -1,5 +1,11 @@
 /input/images/Thumbs.db
-/input-cache/org.hl7.fhir.publisher.jar
+/input/profiles
+/input/vocabulary
+/input/extensions
+/input/examples
+/input-cache/
 temp
 template
 output
+_updatePublisher2.bat
+

input/ignoreWarnings.txt

@@ -2,3 +2,6 @@
 
 # The following code systems are external and not supported by terminology server
 Error from server: Unable to provide support for code system http://ihe.net/fhir/ihe.formatcode.fhir/CodeSystem/formatcode
+
+# The following code system should eventually show up in the terminology server
+Code System URI "http://terminology.hl7.org/CodeSystem/hl7-document-format-codes" is unknown so the code cannot be validated