move optical spectroscopy files to applications/base_classes

[lukaspie]

This brings back the changes as accepted by NIAC in nexusformat#1425

Summary by Sourcery

Move optical spectroscopy application and base class definitions into their appropriate applications and base_classes directories and clean up outdated metadata

Enhancements:

• Relocate NXraman, NXoptical_spectroscopy, and NXellipsometry application definitions from contributed_definitions to applications
• Move NXoptical_window, NXbeam_transfer_matrix_table, and NXwaveplate definitions into base_classes
• Remove obsolete commented TODO blocks and draft metadata from relocated YAML and XML files
• Update SHA hash values to reflect the moved definitions

Documentation:

• Fix minor typos in documentation text

[sourcery-ai]

Reviewer's Guide

This PR reorganizes the optical spectroscopy definitions by relocating application and base‐class YAML and NXDL files into the new applications/ and base_classes/ directories, and cleans up legacy comments and metadata.

Class diagram for updated location of optical spectroscopy base classes and applications

classDiagram
    class NXoptical_spectroscopy {
        <<application>>
    }
    class NXraman {
        <<application>>
    }
    class NXellipsometry {
        <<application>>
    }
    class NXoptical_window {
        <<base_class>>
    }
    class NXbeam_transfer_matrix_table {
        <<base_class>>
    }
    class NXwaveplate {
        <<base_class>>
    }
    NXraman --|> NXoptical_spectroscopy
    NXellipsometry --|> NXoptical_spectroscopy
    NXoptical_window --|> NXaperture
    NXbeam_transfer_matrix_table --|> NXobject
    NXwaveplate --|> NXcomponent
    %% Note: Only class locations and inheritance are shown, as the PR is a reorganization.

Loading

File-Level Changes

Change	Details	Files
Reorganize application definitions	Move NXraman, NXoptical_spectroscopy, NXellipsometry YAML files to applications/nyaml Move corresponding NXDL group definitions to applications/	applications/nyaml/NXraman.yaml applications/nyaml/NXoptical_spectroscopy.yaml applications/nyaml/NXellipsometry.yaml applications/NXraman.nxdl.xml applications/NXoptical_spectroscopy.nxdl.xml applications/NXellipsometry.nxdl.xml
Reorganize base class definitions	Move NXoptical_window, NXbeam_transfer_matrix_table, NXwaveplate YAML to base_classes/nyaml Move corresponding NXDL definitions to base_classes/	base_classes/nyaml/NXoptical_window.yaml base_classes/nyaml/NXbeam_transfer_matrix_table.yaml base_classes/nyaml/NXwaveplate.yaml base_classes/NXoptical_window.nxdl.xml base_classes/NXbeam_transfer_matrix_table.nxdl.xml base_classes/NXwaveplate.nxdl.xml
Clean up and update metadata	Remove outdated draft/TODO comment blocks Refresh SHA hash comments to match new revisions Fix minor typos (e.g., duplicate words)	applications/nyaml/NXraman.yaml applications/nyaml/NXoptical_spectroscopy.yaml applications/nyaml/NXellipsometry.yaml applications/NXraman.nxdl.xml applications/NXoptical_spectroscopy.nxdl.xml applications/NXellipsometry.nxdl.xml base_classes/nyaml/NXoptical_window.yaml base_classes/nyaml/NXbeam_transfer_matrix_table.yaml base_classes/nyaml/NXwaveplate.yaml base_classes/NXoptical_window.nxdl.xml base_classes/NXbeam_transfer_matrix_table.nxdl.xml base_classes/NXwaveplate.nxdl.xml

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[mkuehbach]

These updates on the definitions are consistent with what I found that needs to be carried over from the NIAC, so this lgtm.

Only one question though: What happened to the optical_spectroscopy.rst in the coordinating context descriptions in contributed_definitions?
Do you plan to copy this over with the others later?

[lukaspie]

Only one question though: What happened to the optical_spectroscopy.rst in the coordinating context descriptions in contributed_definitions? Do you plan to copy this over with the others later?

I will only touch the rst files in nexusformat#1428 and then move them over later, it doesn't make sense to make changes here that will anyway be overwritten again in that PR.

[mkuehbach]

doing it with nexusformat#1428 is fine for the rst part