Apply JMS naming strategy consistenly if available

This commit makes sure that if the JMS parser is used, it properly uses
the naming strategy and applies a possibly different name to all parameters, requirements and filters if applicable.

Changes:

- The JMS parser no longer replaces the property name, because
  that will cause duplicate property keys (e.g. camelCase and with
  underscores)
- if the serialized name differs form the property name, it is saved
  with the key 'alias' in the property data
- The ApiDoc::toArray() method now applies aliases to any property name
  if an alias exists in the property data.