Add logging to transport error state from individual tools to the final consumer

### Feature Description

The current pipeline does not allow for the individual tools to forward their error states and warnings.

The pipeline should accept a PSR-3 logger that gets forwarded to the tools, where they can provide error states, warnings and debug messages in a standardized way.

No files or tests are named. Start by locating the pipeline entry point and the interfaces for individual tools, then trace how results reach the final consumer; done means a PSR-3 logger is accepted by the pipeline, forwarded to tools, and exposes their errors, warnings, and debug messages to the consumer.

Written by the indexing model from the issue text.