fix(cli): resolve DB identity on delegated worktree updates (#746)

[paarthsikka]

• Strip REPOWISE_DB_URL from os.environ during delegated run_update so it honors the copied DB
• Add atomic try/except rollbacks to seed staging and rename phases
• Guard sweep_stale_seed_backups with an mtime staleness check
• Pass full=False instead of full=force to prevent re-embedding everything on update
• Skip updating entirely when dry_run=True to prevent bogus output
• Persist --coverage setting explicitly provided in init to config.yaml

Summary

• Resolves a bug ([Bug] worktree seed + delegated update writes new-file pages to the wrong DB / repo identity (not a selection-budget issue) #746) where delegated worktree seeds incorrectly wrote to the base DB by actively stripping inherited environment variables.
• Hardens the worktree .repowise replacement with multi-pass atomic rollbacks to prevent corrupted partial directory states upon failure.
• Ensures the --coverage flag persists successfully during init across full-state rewrites, locked down with a new integration test.

Related Issues

Fixes #746
Builds on #747

Test Plan

• Tests pass (pytest)
• Lint passes (ruff check .)
• Web build passes (npm run build) (if frontend changes)

Checklist

• My code follows the project's code style
• I have added tests for new functionality
• All existing tests still pass
• I have updated documentation if needed

[repowise-bot]

✅ Health: 7.6 (unchanged)

📋 At a glance
1 file changed health · 4 hotspots touched · 5 new findings introduced · 5 co-change pairs left out · 3 files with recent fix history.

Files & modules (2)

• packages (3 files)
  • .../cli/worktree.py
  • .../init_cmd/command.py
  • .../update_cmd/command.py
• tests (1 file)
  • tests/integration/test_cli.py

⚠️ Change risk: moderate _{(riskier than 39% of this repo's commits · raw 8.3/10)}
This change's risk is driven by:

• more lines added than baseline
• more scattered than baseline

🩹 Review priority _{(files here with the most recent bug-fix history — defects cluster, so review these first)}

• tests/integration/test_cli.py — fixed 5× in the last ~6 months
• .../update_cmd/command.py — fixed 5× in the last ~6 months
• .../init_cmd/command.py — fixed 3× in the last ~6 months

File	Score	Δ	Why
.../cli/worktree.py	8.3 → 5.7	▼ -2.6	🔻 introduced nested complexity, error handling, primitive obsession · ✅ resolved io in loop

💡 .../cli/worktree.py: Flatten the control flow. Pull early-return guards to the top, extract the deepest branch into a helper, and consider replacing nested conditionals with a strategy table or dispatch dict.

🔎 More signals (2)

🔥 Hotspots touched (4)

• .../cli/worktree.py — 1 commits/90d, 3 dependents · primary owner: Raghav Chamadiya (100%)
• .../init_cmd/command.py — 19 commits/90d, 1 dependents · primary owner: Raghav Chamadiya (93%)
• tests/integration/test_cli.py — 9 commits/90d, 1 dependents · primary owner: Raghav Chamadiya (48%)

1 more

• .../update_cmd/command.py — 19 commits/90d, 4 dependents · primary owner: Raghav Chamadiya (90%)

🔗 Hidden coupling (2 files)

• .../init_cmd/command.py co-changes with these files (not in this PR):
  • docs/CLI_REFERENCE.md (9× — 🟢 routine)
  • .../init_cmd/workspace.py (7× — 🟢 routine)
  • docs/USER_GUIDE.md (5× — 🟢 routine)
• .../update_cmd/command.py co-changes with these files (not in this PR):
  • .../update_cmd/persistence.py (8× — 🟢 routine)
  • docs/CLI_REFERENCE.md (6× — 🟢 routine)

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📊 Full report · ⭐ Star Repowise · 📥 Install bot · Last updated 2026-07-17 10:06 UTC
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[RaghavChamadiya]

Nice fix on the DB identity leak, but two blockers before merge:

1. save_config_partial(repo_path, coverage=coverage_pct) writes a float under the coverage key, which is already used for the coverage-report ingestion block (CoverageConfig.from_repo_config expects a dict there and silently falls back to defaults if it isn't). It also isn't read back anywhere on update, so it clobbers real config without doing anything. Needs a different key (e.g. coverage_pct) plus a reader in run_update, or drop the persistence.
2. The delegation now passes full=False instead of full=force. full was only ever True when the user explicitly passed --force, so this just silently ignores the flag. Please restore full=force.

Smaller things: the new except Exception in the seed staging loop swallows errors with no message (the sibling branches all print a fallback notice); the 1h mtime gate doesn't really work for .repowise.bak.* since rename preserves mtime (keep unconditional sweep for those, gate only the seed temp dirs); the env-strip loop should reuse DB_ENV_VARS from core persistence instead of hardcoding the tuple; and there are a few trailing-whitespace lines that ruff format will churn.