fix(verify): restore reliable local checks

[barad1tos]

── Summary ─────────────────────────────────

SQLite 3.54 can exit after the setup commands when -bail is present, leaving the note change query unexecuted. Two end-to-end verification tests also read the operator's daemon log, which makes the suite depend on host log size. This restores semantic change detection and makes local verification repeatable.

── Changes ─────────────────────────────────

• Fix: sqlite_token.go:24 — Let the positional query run while retaining read-only access and nonzero exits for SQL errors.
• Test: sqlite_token_test.go:13 — Reject a database without Bear tables instead of hashing a successful setup command.
• Test: run_endtoend_test.go:262 — Give the two affected verification scenarios temporary daemon logs.

── Validation ──────────────────────────────

• go test -p=1 -count=1 -race -coverpkg=./... -coverprofile=/private/tmp/noxctl-compatibility-coverage.out -covermode=atomic ./... — passed; total statement coverage 83.9%.
• go build ./... and go vet ./... — passed.
• golangci-lint v2.12.2 run ./... — 0 issues.
• Pre-commit and commit-message hooks — passed.
• IDE inspections for all three changed files — 0 warnings or errors.

── Notes ───────────────────────────────────

No live Bear apply was run. The Go 1.27 toolchain update is a separate follow-up.

Summary by Sourcery

Restore reliable local verification by fixing SQLite change detection and isolating verification tests from host daemon logs.

Bug Fixes:

• Restore reliable SQLite note-change detection by ensuring the query executes while preserving read-only access and SQL error reporting.

Enhancements:

• Make verification end-to-end tests independent of the host daemon log by using isolated temporary logs.

Tests:

• Add coverage for rejecting SQLite databases without the expected Bear schema.

[sourcery-ai]

Reviewer's Guide

The PR restores reliable SQLite-based semantic change detection by allowing the query to execute under read-only mode, adds invalid-schema regression coverage, and makes affected verification tests deterministic by using temporary daemon logs.

Sequence diagram for SQLite note-change token verification

sequenceDiagram
    participant Verify as Verification
    participant Token as SQLiteNoteChangeToken
    participant SQLite as sqlite3
    participant DB as SQLiteDatabase

    Verify->>Token: SQLiteNoteChangeToken(dbPath)
    Token->>SQLite: execute -batch -readonly query
    SQLite->>DB: read Bear schema and note data
    alt valid Bear database
        DB-->>SQLite: semantic note result
        SQLite-->>Token: query output
        Token-->>Verify: change token
    else missing Bear tables
        SQLite-->>Token: SQL error
        Token-->>Verify: nonzero error
    end

Loading

File-Level Changes

Change	Details	Files
Restore SQLite note-change execution while preserving read-only behavior and SQL failure propagation.	Remove the SQLite CLI flag that can terminate after setup commands. Retain batch, read-only, and nonzero SQL-error handling for the positional query.	bear/engine/sqlite_token.go
Add regression coverage for invalid SQLite schemas.	Create a database containing only an unrelated table. Verify token generation rejects databases missing the Bear schema.	tests/bear/engine/sqlite_token_test.go
Isolate verification end-to-end tests from host daemon log state.	Create temporary daemon logs for the bad-output-format and nil-stdout scenarios. Pass those logs through verification options instead of relying on the operator log.	tests/bear/cli/verify/run_endtoend_test.go

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[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-28T19:00:53.967616Z	71494a8	Draft marked ready

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[sourcery-ai]

Hey - I've reviewed your changes and they look great!

Sourcery assessment

Approved.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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