WIP: ENH: Ingest 10 beta modules inline under Modules/Beta/ (stacked on #6085)

[hjmjohnson]

Stacked on #6085. Grafts 10 remote modules inline under
Modules/Beta/<Name>/, preserving upstream git history and blame. 60
first-parent commits (~2k total including merged-in upstream histories).

Modules ingested (in order): Cuberille, Montage, FastBilateral,
GrowCut, MeshToPolyData, BoneEnhancement, AnalyzeObjectLabelMap,
SimpleITKFilters, LabelErodeDilate, BoneMorphometry.

Per-module commit pattern (6 commits × 10 modules):

1. COMP: Bump <M> remote to upstream tip <sha>
2. ENH: Ingest ITK<M> as Modules/Beta/<M> — merge commit with
   --allow-unrelated-histories --no-ff, byte-identical to upstream tip
3. STYLE: Remove non-ITK artifacts from ingested <M> — mechanical
   cleanup (.github/, .clang-format, pyproject.toml, etc.)
4. COMP: Fix pre-commit hook failures for <M> — scoped pre-commit
   autofixes (EOF newlines, trailing whitespace, gersemi, shebang+x)
5. COMP: Remove <M> remote fetch; now inline at Modules/Beta/<M> —
   deletes Modules/Remote/<M>.remote.cmake
6. DOC: Record <M> upstream provenance in beta manifest — writes
   Modules/Beta/<M>.beta.cmake with UPSTREAM_URL/SHA/INGEST_DATE

Local verification: 118/118 beta-module tests pass on a full
reconfigure+build.

Why the graft-then-clean structure

Reviewer concern on #6061 was that consolidating modules erases author
attribution. This PR takes the opposite approach: each ENH: commit is
the raw git merge --allow-unrelated-histories --no-ff of the upstream
tip, producing a merge whose tree is byte-identical to what
itk_fetch_module() would have checked out. Every subsequent change
(STYLE/COMP/DOC) is a mechanical, auditable layer on top.

Blame preservation verified on Cuberille: 17 distinct authors surface
via git blame, walking back to Matt McCormick's 2015 commits in
ITKCuberille.

The pre-commit-fix commit (new step in procedure)

Ingested upstream repos do not satisfy ITK's pre-commit hooks as-is
(EOF newlines, trailing whitespace, gersemi, shebang-executable bits,
etc.). Rather than mangle the ingest merge or the STYLE cleanup, each
module gets a dedicated COMP: Fix pre-commit hook failures for <M>
commit containing only the autofix hunks for that module's tree.

Reproduce per module:

pixi run -e pre-commit pre-commit run \
  --files $(git ls-files Modules/Beta/<M>/)
# Iterate until fixed-point. For shebang-executable failures:
git update-index --chmod=+x <path>

This step is documented in INGESTION_STRATEGY.md (support worktree).

How to verify blame / history preservation

# Commit count under the module roughly matches upstream log:
git log --oneline -- Modules/Beta/Cuberille/ | wc -l

# Blame walks back to original authors, not the ingester:
git blame Modules/Beta/Cuberille/include/itkCuberilleImageToMeshFilter.h

# All unique authors ever to touch the module:
git log --format='%an' -- Modules/Beta/Cuberille/ | sort -u | wc -l

# No itk_fetch_module() entries remain for ingested modules:
git grep -n itk_fetch_module Modules/Remote/

Future work (post-merge)

• Tier 3 ingests: MorphologicalContourInterpolation, RLEImage, and
  any other pure-C++ remote modules. Same recipe.
• External-dependency modules deferred: CudaCommon (CUDA),
  VkFFTBackend (Vulkan), IOTransformDCMTK (DCMTK), IOOpenSlide
  (OpenSlide), SCIFIO (Bio-Formats). These need build-time optional
  dependency handling that this PR doesn't address.
• Post-hoc cull candidates flagged in INGEST_LOG.md:
  SimpleITKFilters (one adapter file), AnalyzeObjectLabelMap (legacy
  format), BoneMorphometry (large doc/ tex artifacts),
  BoneEnhancement (overlaps with existing enhancement filters).
• Split option: if reviewers prefer, this PR can be split into 10
  per-module PRs. The commit history is already clean per-module; the
  bundled PR is a reviewer-ergonomics choice, not a structural one.

Verification commands (run locally)

# Configure all beta modules ON:
cmake -B build -S . \
  -DModule_Cuberille=ON -DModule_Montage=ON -DModule_FastBilateral=ON \
  -DModule_GrowCut=ON -DModule_MeshToPolyData=ON -DModule_BoneEnhancement=ON \
  -DModule_AnalyzeObjectLabelMap=ON -DModule_SimpleITKFilters=ON \
  -DModule_LabelErodeDilate=ON -DModule_BoneMorphometry=ON

cmake --build build -j$(nproc)

ctest -j4 --test-dir build \
  -R "Cuberille|Montage|FastBilateral|GrowCut|MeshToPolyData|BoneEnhancement|AnalyzeObjectLabelMap|SimpleITKFilters|LabelErodeDilate|BoneMorphometry"
# Expect: 118/118 passed.

[greptile-apps]

Too many files changed for review. (2041 files found, 100 file limit)