Fix case-only source path aliases on macOS

[EmanuelFaria]

Summary: Recognize stored and scanned source paths that differ only by case when samefile proves they are the same disk object. Avoid false fail-closed retention warnings, rewrite preserved source_file values to the scanner's current spelling, and keep ambiguous casefold collisions fail-closed. Regression coverage: simulated APFS case-alias test; real macOS case-insensitive filesystem acceptance; full tests/test_watch.py passed with 85 passed and 2 skipped; ruff passed.

[graphify-labs]

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

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Graphify review — findings

This PR adds case-insensitive path alias handling to the graph reconciliation logic in graphify/watch.py. When a stored node's source path differs only by letter case from a currently scanned file, the code now attempts to confirm they point to the same on-disk file via os.path.samefile(), and if so treats the stored path as current rather than excluded—rebasing it to the scanner's canonical spelling. It also extends rebase_preserved to accept a mapping of canonical identities and builds a casefold lookup that discards ambiguous case-only collisions. On the test side, it adds test_reconcile_case_alias_uses_current_source_spelling, which monkeypatches samefile to simulate APFS case-insensitive behavior on case-sensitive CI and asserts the preserved node adopts the scanner's spelling without a fail-closed warning. The large set of renamed rationale_* test symbols appears to reflect surrounding test-file churn rather than substantive logic changes.

No blocking issues surfaced. 2 lower-confidence candidates did not survive cross-model review.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 363 functions depend on the 233 functions this change touches.

Health — this change adds coupling hotspots:

• worse: _reconcile_existing_graph() — 3 callers, 10 callees

Verification — 363 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 237 function(s) in the blast radius were not formally verified this run

· 1 more finding(s) on lines outside this diff (see the check run).