Clear the regenerator cache every time we process

To address part of #3591, clear the regenerator's cache every time the
site is processed. This ensures that the regenerator doesn't incorrectly
believe a file hasn't changed based on stale information.

lib/jekyll/regenerator.rb

@@ -59,6 +59,14 @@ module Jekyll
       @cache = {}
     end
 
+
+    # Clear just the cache
+    #
+    # Returns nothing
+    def clear_cache
+      @cache = {}
+    end
+
     # Checks if a path's (or one of its dependencies)
     # mtime has changed
     #

lib/jekyll/site.rb

@@ -68,6 +68,7 @@ module Jekyll
       self.static_files = []
       self.data = {}
       @collections = nil
+      @regenerator.clear_cache()
 
       if limit_posts < 0
         raise ArgumentError, "limit_posts must be a non-negative number"