Merge datasec changes with bump to python 3.13

[jwlodek]

• WIP changes from 6/30/25 pair coding
• Fix io server message
• Add bluesky install task to pixi.toml
• Support filling the directory from start doc
• numpy compat with np.bool_
• Add missing pypi packages
• Install pdfsteam from GitHub (static)
• Update the pixi.lock file
• Bump python version to 3.13, update scikit-beam to compatible version.

[jwlodek]

All the changes from the working datasec version, plus a bump to 3.13 now that we have the 3.13 and 3.12 wheels for diffpy.pdfgetx. Tested at the beamline and confirmed that it is working.