Negative numbers are supported. But if you want a clean solution, implementing a SubtractionOperator is easy enough. Just implement the OperatorInterface.
The library supports adding other numbers than 1 and 1. Your use case of adding 2 to 1 is supported. As are multi-digit numbers. As are negative numbers.
Many people asked for yaml support in composer, and it was shot down. Here's why: Once you start supporting many formats you lose interoperability, as any tooling now needs to support all formats. That is the main reason why composer will not support sexpr.
xdebug exposes a gdbp interface which supports breakpoints, stepping, inspecting variables, etc. And you can use it with gdb or any GUI that supports gdbp, such as macgdbp.
EDIT: It does not expose a REPL though, which I suppose is what you meant?
Yeah, the lack of native non-blocking bindings is quite the issue. There have been some attempts at implementing plain-PHP non-blocking drivers. One of the most impressive I've seen so far is phpdaemon: https://github.com/kakserpom/phpdaemon.
This is an excellent example of how _not_ to write code.
Custom autoloading scheme instead of PSR-0? Classname.inc.php, seriously? Moving on, dynamic variables are a terrible unfeature that should be avoided. References usually cause more harm than good and should be avoided as well. And finally, a class which is named with a redundant "Class" suffix, containing only static members, aka class-oriented programming.