Update some documentation

lib/brakeman/call_index.rb

 require 'set'
 
+#Stores call sites to look up later.
 class Brakeman::CallIndex
+
+  #Initialize index with calls from FindAllCalls
   def initialize calls
     @calls_by_method = Hash.new { |h,k| h[k] = [] }
     @calls_by_target = Hash.new { |h,k| h[k] = [] }
@@ -10,6 +13,14 @@ class Brakeman::CallIndex
     index_calls calls
   end
 
+  #Find calls matching specified option hash.
+  #
+  #Options:
+  #
+  #  * :target - symbol, array of symbols, or regular expression to match target(s)
+  #  * :method - symbol, array of symbols, or regular expression to match method(s)
+  #  * :chained - boolean, whether or not to match against a whole method chain (false by default)
+  #  * :nested - boolean, whether or not to match against a method call that is a target itself (false by default)
   def find_calls options
     target = options[:target] || options[:targets]
     method = options[:method] || options[:methods]

lib/brakeman/checks/check_execute.rb

@@ -25,7 +25,7 @@ class Brakeman::CheckExecute < Brakeman::BaseCheck
     end
   end
 
-  #Processes results from FindCall.
+  #Processes results from Tracker#find_call.
   def process_result result
     call = result[:call]
 

lib/brakeman/checks/check_sql.rb

@@ -37,7 +37,7 @@ class Brakeman::CheckSQL < Brakeman::BaseCheck
     end
   end
 
-  #Process result from FindCall.
+  #Process result from Tracker#find_call.
   def process_result result
     call = result[:call]
 

lib/brakeman/tracker.rb

@@ -97,6 +97,26 @@ class Brakeman::Tracker
   end
 
   #Find a method call.
+  #
+  #Options:
+  #  * :target => target name(s)
+  #  * :method => method name(s)
+  #  * :chained => search in method chains
+  #
+  #If :target => false or :target => nil, searches for methods without a target.
+  #Targets and methods can be specified as a symbol, an array of symbols,
+  #or a regular expression.
+  #
+  #If :chained => true, matches target at head of method chain and method at end.
+  #
+  #For example:
+  #
+  #    find_call :target => User, :method => :all, :chained => true
+  #
+  #could match
+  #
+  #    User.human.active.all(...)
+  #
   def find_call options
     index_calls unless @call_index
     @call_index.find_calls options

lib/brakeman/warning.rb

@@ -5,7 +5,7 @@ class Brakeman::Warning
 
   attr_accessor :code, :context, :file, :message
 
-  #+options[:result]+ can be a result Sexp from FindCall. Otherwise, it can be +nil+.
+  #+options[:result]+ can be a result from Tracker#find_call. Otherwise, it can be +nil+.
   def initialize options = {}
     @view_name = nil