Bug fixes about template parse etc.

Intensive bug fixes have been conducted, including correctness of regular
expression for matching codes and template instance (including associated
instance).
Bug fixes for parse subcommand

Bugs:
- CodeEntity should read origin path.
- Internal dependency that is parsed is no longer a symbol, but CodeEntity.

News:
- Remove "parse" method in Project.
- "parse" subcommand of CodeMate now parses templates.