adding logging functionality to run protocol / experimental protocols

[mbreiser]

should add spec details for logging functionality: include a default logging of every executed command w. timestand (always nice to have, but esp. critical for randomized trials) and also some flexibility for user-specified logged responses from the plugin commands (e.g. @leburnett logs current frame from BIAS)/

[floesche]

In addition we could add a "type" "log" that allows storing arbitrary messages during the protocol.

For example:

block:
  conditions:
    # --------------------------------------------------------------------------
    # Condition 1: Background Light Activation with Pattern Display
    # --------------------------------------------------------------------------
    # Demonstrates combined device control and pattern presentation.
    # This condition opens the iris, activates background lighting,
    # then displays a visual pattern.

    - id: "activate_background"
      commands:
        # Open iris to 50mm diameter
        - plugin: "flyris"
          method: "open_mm"
          params:
            width: "50mm"

        - type: "log"
          message: "Flyris set to 50mm width"
        # Activate red background light
        - plugin: "background_light"
          command: "activate"

This becomes particularly useful when using "store_as" syntax as described in #3.

[taylorlm88]

default logging functionality is implemented. Custom, plugin-specific logging will be added with plugin implementation, still coming.