Mw/fix/plugin management

[micahpw]

• Adds plugin level logging [{plugin name}] to the r2x.log or terminal.
• Adds a --no-stdout option to avoid printing system json being passed between plugins.
• Adds package version in output of r2x list. Adds path if installed from local directory.
• Small fixes to handle passing positional arguments of plugins.
• Fixed plugin removal to completely remove package from manifest. Avoids future installation issues.

[micahpw]

@pesap Instead of --no-stdout should we default to hiding stdout and instead let users pass something like --log-stdout in the off chance they want to see the system json in the terminal?