Made status --check decide .gitignore presence with the writer's CR-blind test

[dzykovic]

Summary

Closes #45. status --check checked each adapter's .gitignore patterns with its own grep -Fqx. On Linux and macOS a CRLF .gitignore keeps the \r on every line, so present patterns were reported missing, while the .gitignore writer treats them as present — intelligence init changed nothing and the finding never cleared. Git Bash on Windows hid it, because MSYS grep drops the CR.

The writer's presence test, ignore_file_has_line (cli/lib/gitignore.sh), is now the only one: a Bash read loop that strips exactly one trailing CR — as Git itself does — compares literally, and handles a last line without a newline. status --check calls it for ignore and include patterns. The rule text in intelligence/rules/shell.md that claimed "a \r is part of the pattern Git matches" was wrong (Git drops one trailing CR per line; checked on git 2.43 and 2.54) and is corrected, with a pointer to the shared test.

Type of change

• CLI lifecycle or package behavior
• Sync engine or adapter
• Rule, agent, or skill content
• Documentation
• Refactor with no behavior change

Public CLI check

• Uses only the established public command groups (no command changes)
• Keeps preview/apply behavior explicit for planned writes (unchanged)
• Covers automatic project alignment and CI refusal through the existing suites
• Keeps fresh-clone package restoration behind intelligence sync (unchanged)

Verification

Run on Linux, macOS or WSL — on Git Bash grep hides the CR and the old behaviour cannot be observed. Work in a scratch directory outside this checkout; nothing below moves the checkout or its refs. Lay out this branch's runtime first: mkdir rt && git -C <checkout> archive <this PR's head> cli engine packages | tar -x -C rt, and use bash rt/cli/intelligence as the CLI.

1. git init proj and run init --targets claude in proj. Expected: exit 0; status --check exits 0.
2. Rewrite proj/.gitignore with CRLF endings in Bash (while IFS= read -r l; do printf '%s\r\n' "$l"; done < .gitignore > g && mv g .gitignore) and delete its CLAUDE.md line. Expected: status --check exits non-zero and names only CLAUDE.md as missing — not .claude/* or !.claude/settings.json, which are still there.
3. Run init --no-sync. Expected: exit 0; CLAUDE.md is back exactly once and every line of .gitignore still ends in CR; status --check exits 0. A second init --no-sync leaves .gitignore byte-identical.

Automated coverage

• e2e-negative section 15 runs the steps above on a CRLF .gitignore built in Bash; against the old check.sh in WSL it fails — status --check reported three patterns missing and still "3 problem(s)" after init.
• unit-gitignore pins ignore_file_has_line: matches with or without the CR including an unterminated last line, no prefix/substring/glob matching, only one CR stripped, a missing file is false.
• bash cli/tests/verify.sh (scope all, run in WSL) printed verify ok.

Versioned artifacts

• v0.18.1 is published, so this selects 0.19.0, the version every open release PR shares
• Engine version, example schema versions, exact sync pins and their lock entries moved together
• CHANGELOG.md has its line under ## [0.19.0]
• No stable release is published by this PR

Notes for reviewers

Other grep-style presence checks in cli/ were audited and read LF output the CLI or engine wrote, or validated records; only the .gitignore checks read a CRLF-capable project file.

[Copilot]

Copilot review overview

🟢 Approval recommended

The shared CR-aware implementation, regression coverage, and lockstep release artifacts are consistent with the repository contracts.

Review effort: Balanced
Findings: None

What changed in this PR

Fixes #45 by aligning status --check with the CRLF-aware .gitignore writer.

Changes:

• Reuses ignore_file_has_line for Git policy checks.
• Adds unit and end-to-end CRLF regression coverage.
• Updates release artifacts and CR-handling guidance for 0.19.0.

File	Description
CHANGELOG.md	Records the CRLF fix.
cli/​internal/​check.sh	Uses the shared presence test.
cli/​lib/​gitignore.sh	Implements literal, CR-aware line matching.
cli/​tests/​e2e-negative.sh	Covers CRLF lifecycle behavior.
cli/​tests/​unit-gitignore.sh	Tests exact matching and edge cases.
engine/​VERSION	Advances the engine to 0.19.0.
intelligence.yaml	Updates schema and sync package versions.
intelligence.lock	Updates locked engine and sync versions.
intelligence/​rules/​shell.md	Corrects CR handling guidance.
examples/​cli-project/​intelligence.yaml	Updates version pins.
examples/​dotnet-api-with-react-frontend/​intelligence.yaml	Updates version pins.
examples/​dotnet-api-with-react-frontend/​intelligence.lock	Updates locked versions.
examples/​go-api/​intelligence.yaml	Updates version pins.
examples/​go-api/​intelligence.lock	Updates locked versions.
examples/​go-api-with-antigravity/​intelligence.yaml	Updates version pins.
examples/​go-api-with-antigravity/​intelligence.lock	Updates locked versions.
examples/​go-api-with-opencode/​intelligence.yaml	Updates version pins.
examples/​go-api-with-opencode/​intelligence.lock	Updates locked versions.
examples/​go-api-with-pi-and-codex/​intelligence.yaml	Updates version pins.
examples/​go-api-with-pi-and-codex/​intelligence.lock	Updates locked versions.
examples/​platform-with-submodules/​intelligence.yaml	Updates version pins.
examples/​platform-with-submodules/​intelligence.lock	Updates locked versions.
examples/​with-remote-skills/​intelligence.yaml	Updates version pins.

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[dzykovic]

Verification - PASS

head: 8034dc5 - steps: PR "Verification" section, steps 1-3 (qa_checks: no match, docs/qa-checks.md does not exist) - env: local

Built from the head commit only: git archive 8034dc5 cli engine packages into a scratch dir outside the checkout, run via bash <rt>/cli/intelligence. Ran in WSL per the PR's own instruction and this host's note that Git Bash's MSYS tools hide the CR this change fixes.

#	Step	Source	Verdict	Observed
1	git init proj; init --targets claude in proj. Expected: exit 0; status --check exits 0.	PR	pass	Both exited 0; status --check printed "all good."
2	Rewrite proj/.gitignore CRLF, delete its CLAUDE.md line. Expected: status --check exits non-zero, naming only CLAUDE.md missing.	PR	pass	Fixture confirmed every line CRLF with no CLAUDE.md line before the check. status --check exited 1 with exactly one finding: adapter 'claude' Git policy is missing 'CLAUDE.md'. .claude/* and !.claude/settings.json were not reported.
3	init --no-sync. Expected: exit 0; CLAUDE.md back exactly once, every line still CR-terminated; status --check exits 0; a second init --no-sync leaves .gitignore byte-identical.	PR	pass	Exit 0; CLAUDE.md present exactly once, all 6 lines CRLF. status --check printed "all good." (exit 0). Second init --no-sync produced a byte-identical .gitignore (cmp -s true).

Negative probes (boundary this change names, beyond the declared steps)

• Double trailing CR on the CLAUDE.md line (CLAUDE.md\r\r): ignore_file_has_line strips exactly one CR, so this should not match. Observed: reported missing, exit 1 — matches the documented one-CR-only contract.
• Last .gitignore line CR-terminated with no trailing newline at EOF: observed status --check still recognized it as present, exit 0 ("all good") — matches the diff's claim of handling a last line without a newline.
• Empty .gitignore (0 bytes): all three managed patterns reported missing, no crash, exit 1.

No defects found in the declared steps or the probes.

No standing checks applied — profile qa_checks resolves to docs/qa-checks.md, which does not exist in this repository.

[dzykovic]

Code review - CLEAN

head: 8034dc5 - base: main - files 23, +142/-61

No Critical, Warning, or Suggestion findings.

Verified: ignore_file_has_line (cli/lib/gitignore.sh) is now the single presence test for ignore/include patterns, called from both the writer and status --check (cli/internal/check.sh:159,163); unit-gitignore.sh and the new e2e-negative CRLF scenario (both re-run here, plus once under real WSL/Linux grep semantics) pass; shellcheck at the project's --severity=warning gate is clean on every touched file; all version-lockstep files (engine/VERSION, every example's schema_version/pin, CHANGELOG.md) move together and match the already-published-0.18.1 -> pending-0.19.0 selection shared with open PR #54; the rule correction in intelligence/rules/shell.md points at the one shared implementation instead of restating it; commits are split one-logical-change-per-commit; no other grep-based presence check in cli/ reads a project file that can carry CRLF (the rest read CLI/engine-generated output or do substring, not exact-line, matching). PR body claims all have matching code in the diff, and nothing here contradicts the existing "Verification - PASS" comment on this head.