fix(workflows): match overlay file extensions case-insensitively

[jawwad-ali]

Problem

ProjectOverlaySource.collect matches the extension verbatim:

if not path.is_file() or path.suffix not in (".yml", ".yaml"):
    continue

So a hand-placed overlay named <id>.YML or <id>.Yaml is skipped and never applied — and nothing is reported to say the file was ignored. Overlay files are explicitly hand-authored (docs/reference/workflows.md documents the format and tells users to write them), so the extension casing is the author's choice, not something the tool generated.

Reproduction (before the fix)

Three overlays in one directory, differing only in extension case:

files on disk: ['Mixed.Yaml', 'UPPER.YML', 'lower.yml']
COLLECTED    : ['lower']
SKIPPED      : ['mixed', 'upper']

The author gets no error and no warning — the overlay simply has no effect.

Why this is the odd one out

Every other YAML discovery path in the package already lowercases before matching:

location	form
workflows/engine.py (WorkflowEngine.load_workflow)	path.suffix.lower() in (".yml", ".yaml")
workflows/command_add.py (two sites)	dev_path.suffix.lower() / source_path.suffix.lower()
workflows/command_run.py	source_path.suffix.lower() in (...)
workflows/overlay/layer_sources.py (ProjectOverlaySource.collect)	path.suffix in (...) ← this PR
workflows/overlay/operations.py (_find_overlay_file)	path.suffix in (...) ← this PR

Fix

Lowercase the suffix in both overlay paths, so the resolver and the management commands agree on which files are overlays:

if not path.is_file() or path.suffix.lower() not in (".yml", ".yaml"):

• ProjectOverlaySource.collect — a <id>.YML overlay is now applied.
• _find_overlay_file (added at @mnriem's request) — the same overlay is now reachable by workflow overlay enable / disable / remove. Fixing only the loader would have left it applied, but impossible to manage: every management command reported it "not found".

Verification

• Loader: tests/workflows/test_overlay_layer_sources.py, parametrized over .YML, .Yaml, .YAML, .Yml. All 4 fail with the source reverted to main and pass with the fix. A companion test asserts that broadening the case did not broaden which extensions are accepted: notes.txt, backup.yml.bak, README.md and data.json are still skipped.
• Management commands: one focused test per command in its mirrored suite (tests/specify_cli/workflows/overlay/test_command_disable.py, test_command_enable.py, test_command_remove.py), each parametrized over lint.YML / lint.Yaml. All 6 fail with the source reverted to main and pass with the fix.
• Scoped regression over tests/workflows, tests/specify_cli/workflows/overlay and test_command_resolve.py: 235 passed. The 10 failures are the same pre-existing Windows symlink-privilege tests that fail on unmodified main; none are new.
• uvx ruff@0.15.0 check src tests → clean.

Behaviour change, disclosed: files previously skipped now get read, and the overlay management commands now find them. If a project already holds a .YML/.YAML file in an overlay directory that is not a valid overlay manifest, resolution will now report it rather than ignoring it — which is the intended outcome, but it is a change for such a project.

---

Written with assistance from Claude Code. Bug found, reproduced, and verified by me on current main.

🤖 Generated with Claude Code

[mnriem]

Please include the corresponding case-insensitive check in _find_overlay_file() here. Otherwise these overlays become active while the management commands cannot locate them.

Add coverage showing that an uppercase-extension overlay can also be disabled, removed, and have its priority changed. This completes the same behavior fix rather than expanding scope.

Coordinate with #4141 through normal rebasing—whichever lands later should reconcile with the earlier change.

Drafted for @mnriem with assistance from GitHub Copilot (model: GPT-6 Astra; interactive comment drafting).

[Copilot]

🟡 Changes recommended

Overlay management commands still cannot find uppercase-extension overlays accepted by resolution.

Get a fresh assessment by requesting another Copilot review.

Pull request overview

Updates project overlay discovery to accept case-insensitive YAML extensions.

Changes:

• Normalizes overlay suffixes before matching.
• Adds regression and rejection tests.

File summaries

File	Description
src/specify_cli/workflows/overlays/layer_sources.py	Adds case-insensitive extension matching.
tests/workflows/test_overlay_layer_sources.py	Tests mixed-case YAML and rejected extensions.

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Balanced

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[mnriem]

Please address Copilot feedback and resolve conflicts

[jawwad-ali]

@mnriem Conflicts resolved and feedback addressed (06f9932). Both halves are in: ProjectOverlaySource.collect in workflows/overlay/layer_sources.py and the matching case-insensitive check in _find_overlay_file() (workflows/overlay/operations.py) you asked for, so an uppercase-extension overlay that the resolver applies is also reachable by overlay enable/disable/remove.

tests/workflows/test_overlay_commands.py was split on main, so the management test now sits in tests/specify_cli/workflows/overlay/test_command_list.py beside the other _find_overlay_file tests. I also replaced a source comment that cited _commands.py line numbers, since that file no longer exists.

Verified: 6 new cases fail with both sources reverted to main and all pass with the fix.

Rebased as a single commit on current main; uvx ruff@0.15.0 check src tests is clean. Any remaining local failures are the pre-existing Windows symlink-privilege tests, which fail identically on unmodified main.

[Copilot]

Copilot review overview

🟡 Changes recommended

The new multi-command regression test is placed in the list command’s dedicated test suite, contrary to the repository’s mirrored test structure.

Review effort: Balanced
Findings: 1

Open (1)

• Place regression test in the appropriate command suite · New

Resolved since last review (1)

• This makes an uppercase-extension overlay active during resolution, but _find_overlay_file in…

[mnriem]

Please address Copilot feedback

[jawwad-ali]

@mnriem Copilot feedback addressed in 324dfef, and the thread is resolved. Per design/cli.md's mirrored test layout, the regression test now lives in the per-command suites (test_command_disable.py, test_command_enable.py, test_command_remove.py), one focused test each over lint.YML / lint.Yaml, and test_command_list.py is back to its main content. All 6 cases fail with the source reverted and pass with the fix; there are no new failures across the overlay suites, and ruff is clean. I also refreshed the PR description, which still said _find_overlay_file was out of scope.

[Copilot]

🟡 Changes recommended

The shared lookup change also affects add and set-priority, but those command paths lack regression coverage.

1 open finding

• Add uppercase-extension regression tests for add and set-priority · New

1 resolved since last review

• Place regression test in the appropriate command suite

🧠 Review effort: Balanced

[mnriem]

Please address Copilot feedback