[2.0][DDC-354][DDC-425] Fixed. Encapsulated SQL logging better in the DBAL. Added binding types to DBAL mapping types as well as using these binding types in the persisters. Query and NativeQuery now support PDO binding types as well as DBAL mapping types when binding parameters.

[2.0] More docblocks. Renamed methods Type::addCustomType to Type::addType and Connection::exec to Connection::executeUpdate. Added Type::hasType.

Started refactoring in DQL parser to separate Production into Parser and AST classes.
Finished first tests. Currently only 4 are active in IdentifierRecognitionTest, and only 2 are passing.

reverting the reorganization done in 3455-3456 in order to make merging my experimental branch to trunk easier.

Preparation for new organization of code in to sub packages. Changed autoload() to work with new structure.

- Fixed problem with Nested Set table definition not happening in time for exporting when NestedSet behavior is added through Doctrine_Template_NestedSet.

- Removed the reserved alias "base" from the nested set. It's no longer necessary to use that. Use whatever alias you want.

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removing the closing PHP tags form all php files, it\'s not needed and can break sessions which are whitespace sensitive

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