skpkg: recut the package using latest skpkg-version

[stevenhua0320]

@sbillinge ready to review. Mostly are made by the skpkg update command with minimal fix. In this PR:

1. Because we don't want to change license, I maintained the same one as before. And also the same for the license starting date. I manually add the starting year of license.
2. I realized that in the matlab code, one of the parameters should be called alpha instead of alph. Therefore, I changed that to the correct name.
3. To make it convenient to update, since originally we have the doc instead of docs, I first did a rename of the folder so that package update would identify the structure and do the update for the docs folder properly.
4. If this could be merged, I would do the pytest stuff to update the deprecation thing in the next PR.

[stevenhua0320]

@sbillinge We fail on this because right now we haven't pull diffpy.pdffit2 to python 3.14. We need to wait for Zhiming for some time and then rerun the test so that we could see if it would pass.