COMP: Skip dot-directories when scanning for ITK modules

[hjmjohnson]

itk_module_load_dag() uses GLOB_RECURSE, which matches itk-module.cmake at any depth. Any nested source tree under the ITK checkout is therefore absorbed as a set of duplicate modules and built as if it were part of the project.

Nesting a second tree inside a project is a widespread convention, and it almost always lives under a dot-directory. On one affected workstation this produced 984 discovered modules where 204 exist, and the duplicates broke the build outright.

Why dot-directories, specifically

Dot-directories are the near-universal convention for content that is not project source: version-control internals, tool and editor state, language environments, and caches. A checkout of ITK — or of anything containing */*/*/itk-module.cmake — commonly ends up inside one:

Paradigm	Typical location
Secondary git worktree trees	.worktrees/<branch>/, or a tool-managed directory
Editor / IDE / agent state	.vscode/, .idea/, .vs/, and similar
Language & package environments	.pixi/, .venv/, .tox/, .conda/
Build and download caches	.cache/, .ExternalData/

This is not hypothetical for ITK. ITK's own documented build tool creates .pixi/ inside the source tree — 3.3 GB on the machine where this was found — and .gitignore already declares .pixi and .idea as non-source. The module scan simply does not honor the same convention that the rest of the project already assumes.

The failure is also easy to misread, because the duplicates are built against the outer tree's configuration. A nested checkout on an older branch fails in ways that look like a defect in the tree you are actually working on:

FAILED: .<dot-dir>/<nested-tree>/Modules/Numerics/FEM/src/CMakeFiles/ITKFEM.dir/....o
vnl/algo/vnl_svd.h:13:6: error: #error "vnl/algo/vnl_svd.h is deprecated; migrate to itk::Math::SVD"

The path is the giveaway, but it is easy to miss in a full log, and ninja stops there — a plain ninja in that tree could not complete.

Fix

list(FILTER meta EXCLUDE REGEX "(^|/)\\.")

Scoped deliberately narrowly:

• Matches a dot only at the start of a path component, so directory names that merely contain a dot (ITK.Something) are unaffected.
• The glob is RELATIVE "${ITK_SOURCE_DIR}", so an ITK checkout that itself lives under a dot-path (/home/user/.cache/src/ITK) is unaffected — the absolute prefix is stripped before matching.
• ITK ships no itk-module.cmake under any dot-directory, so nothing in-project is excluded.

Validation

Verified on a tree containing four nested checkouts:

Check	Result
Modules discovered before	984
Excluded by the filter	780
Excluded that were not a nested checkout	0 (no false positives)
Modules discovered after	204
Modules/Remote/* retained	10 of 10

Behavioral check with ITK_FUTURE_LEGACY_REMOVE=ON, ITK_LEGACY_REMOVE=ON, Module_ITKReview=ON, 10 remote modules enabled:

• before: 314 nested targets, ninja -k 0 failed
• after: 0 nested targets, ninja -k 0 exits 0 with zero failures

Had the filter dropped a real module, that build would have failed to link.

Remote modules are unaffected

In-tree: remotes are always fetched to ${ITK_SOURCE_DIR}/Modules/Remote/${_name} (CMake/ITKModuleRemote.cmake), a path the regex cannot match. All 10 enabled remotes are retained above.

Standalone: a remote module built on its own against an installed ITK never reaches this code. ITKModuleEnablement is included only from ITK's top-level CMakeLists.txt and is not installed for downstream consumers, so a module using find_package(ITK REQUIRED) + itk_module_impl() never calls itk_module_load_dag().

[greptile-apps]

Greptile Summary

This PR narrows ITK module discovery to ignore module metadata beneath dot-prefixed directories.

• Filters relative itk-module.cmake paths before constructing the module dependency graph.
• Preserves ordinary in-tree and fetched remote modules while avoiding nested tool-state checkouts.

Confidence Score: 5/5

The PR appears safe to merge with no actionable defects identified.

The filter operates on paths relative to the source root, excludes only dot-prefixed path components, and leaves the repository’s standard and fetched remote module layouts discoverable.

T-Rex Logs

What T-Rex did

• The initial configure attempt failed with exit code 1 because Module_ITKTrexDotModuleFixture:BOOL=OFF appeared in CMakeCache.txt.
• After adjustments, the configure and generate steps completed with exit code 0, and an explicit assertion confirmed Module_ITKTrexDotModuleFixture was absent.
• A positive-control nested fixture produced Module_ITKTrexNormalModuleFixture:BOOL=OFF.
• Remote retention validation confirmed that all 19 remote .remote.cmake declarations had corresponding _REMOTE_COMPLIANCE_LEVEL cache entries.

_{Ran code and verified through T-Rex}

Important Files Changed

Filename	Overview
CMake/ITKModuleEnablement.cmake	Adds a correctly scoped path-component filter to module discovery; no supported module layout or remote-module destination is excluded.

_{Reviews (1): Last reviewed commit: "COMP: Skip dot-directories when scanning..." | Re-trigger Greptile}

[dzenanz]

LGTM, it would be good if someone else reviewed too.