Migrated the container to a wine 11 base without .NET Framework

[chambm]

Summary

Migrates the container to a plain wine 11 base, dropping the custom wine-dotnet
image and its .NET Framework / winetricks layers.

• wine/Dockerfile (new base) — ubuntu:24.04 + winehq-stable 11.0. The OS bump
  is forced, not cosmetic: WineHQ's focal builds stop at 10.6, which is why the old
  base was pinned there. Wine 11 is published for jammy and noble only.
• No .NET Framework, no VC++ redistributables. The net10 payload carries its own
  runtime, and pwiz-sharp deploys the vendor SDKs' VC runtimes app-local. MFC140 was
  the one wine has no builtin for, and was the reason Shimadzu silently returned zero
  spectra without winetricks vcrun2019.
• corefonts kept — that is Skyline font rendering, not a runtime dependency.
• UTF-8 locale set in the base, which clears the CJK Shimadzu failure.
• App image repointed at the new base and at the net10 SkylineTester.zip, which
  carries Skyline, msconvert and the runtime in one artifact; the C++ pwiz-bin tarball
  is dropped since msconvert is now the managed port.

Image is 4.52 GB vs 5.74 GB for wine-dotnet — 1.2 GB smaller.

Two traps worth knowing, both fixed here and both silent:

• wineboot hangs forever on prefix creation because the Mono/Gecko offer is a GUI
  dialog with nobody to answer it. The old base never hit it because winetricks dotnet48 set mscoree to native first. The suppression is scoped to that one RUN
  on purpose: left as a persistent ENV it breaks the payload, which then dies with
  FileNotFoundException ... System.Runtime.dll ... Module not found on every input
  even though the runtime is present and complete.
• wineserver -w after winetricks hangs the build (it waits for a process winetricks
  leaves behind); -k is deterministic.

Test plan

• Base builds; wine-11.0, 31 corefonts incl. Arial, LANG/LC_ALL=C.UTF-8, no
  WINEDLLOVERRIDES persisted into the image env
• App image builds on the new base
• 43-pair vendor sweep inside the built image: 43/43 converted, 40/43 matching
  reference spectrum + chromatogram counts. Validated on counts, never exit codes —
  the failure mode is a structurally valid mzML with no spectrumList
• Shimadzu 10nmol = 150 spectra (the case that returned 0 without the VC runtimes)
• Shimadzu CJK-named fixture matches (UTF-8 locale)
• The 3 count mismatches (2x Mobilion, 1x Waters) are the pre-existing
  reference-generation differences, not regressions

Notes for review

• The payload was exercised with a stand-in SkylineTester.zip built from the current
  msconvert-sharp output plus a bundled .NET 10 runtime; it needs one build against a
  real net10 CI artifact to confirm DOTNET_ROOT=C:\pwiz\skyline\dotnet matches the
  layout the zip actually ships.
• dotnet/Dockerfile is left in place rather than deleted so the old base stays
  buildable; it is unused by this Dockerfile and can be removed once the new base is
  published.
• pwiz-sharp has no msdiff (only MsConvert and MsBenchmark), so any validation
  that shells out to msdiff needs either a port or the C++ tool kept alongside.

Co-Authored-By: Claude noreply@anthropic.com