This reverts commit 87a59675011a4cf284d8e44c4fb66042ad84c39f.
At least 'modules/doc/run.php' issues a warning about "The use statement with non-compound name 'Zend_Controller_Router_Route' has no effect"
- The CommandPipe class now delegates submission of commands to
the Transport classes (LocalPipe or SecureShell)
- Added SSH options for non-interactive mode
- Refactored tests
refs #4441