DEGA-331-Xenium-pre-processing-bug and lower max_workers default to 1

[cornhundred]

This pull request

• reverts API breaking changes to the preprocessing main function
• lowers the default max_workers to 1 (prevents crashing on Manifold notebook)
• adds argument to set max_workers to main function

[Copilot]

Pull Request Overview

This PR addresses a Xenium pre-processing bug (DEGA-331) and reduces the default parallelization from multiple workers to a single worker for improved stability. The main changes focus on fixing path construction issues and adjusting concurrency defaults.

• Fixes data directory path construction by properly joining the sample name to the root directory
• Reduces default max_workers parameter from 2/8 to 1 across preprocessing functions
• Updates documentation to clarify data directory structure requirements
• Removes debugging print statement from local server

Reviewed Changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

File	Description
src/celldega/pre/run_pre_processing.py	Fixes path construction bug and adds max_workers parameter with default of 1
src/celldega/pre/boundary_tile.py	Changes default max_workers from 8 to 1
src/celldega/viz/local_server.py	Removes debug print statement for server port

[cornhundred]

We can test this on a MERSCOPE dataset later since we have another issue that will need to be addressed with that technology #154. For now, we can test on Xenium only.