fix(beads): harden worktree identity checks

[christso]

Summary

AgentV no longer tracks checkout-local Beads identity or live Beads config. The repo keeps only the Beads template (.beads/config.yaml.example) and .beads/.gitignore, while .beads/config.yaml, .beads/metadata.json, and runtime state stay local.

This also removes the stale AgentV workflow note that treated .beads/metadata.json as intentionally tracked. Developer-specific Beads workflow guidance now lives in the shared Beads skill.

Verification

• git diff --check
• bd --readonly config get federation.remote reports git+https://github.com/EntityProcess/agentv-beads.git from the local config
• git ls-files .beads reports only .beads/.gitignore and .beads/config.yaml.example

Post-Deploy Monitoring & Validation

No additional production monitoring required. This is repo coordination config only. After merge, copy .beads/config.yaml.example to .beads/config.yaml in a local checkout, then validate with git ls-files .beads and bd --readonly config get federation.remote.

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View logs

[christso]

Review/dogfood update: PR #1460 is not merge-ready as-is. The focused dogfood pass for the current checkout passed, but the stricter review found two P1 Beads identity/bootstrap regressions:

1. Removing .beads/metadata.json strands existing embedded Dolt data under the wrong database identity. Without metadata, bd falls back to database beads; bd --readonly list returns no issues. Restoring metadata resolves database av and returns real av-* issues.
2. bd bootstrap keys off sync.remote, not federation.remote. Because EntityProcess/agentv still advertises refs/dolt/data, fresh bootstrap can choose the code repo instead of EntityProcess/agentv-beads.

I pushed a stacked draft fix PR here: #1461

That branch adds sync.remote and restores the stable metadata identity behavior; its net diff against origin/main is only .beads/config.yaml adding sync.remote. Verification covered fresh bootstrap, existing embedded-Dolt data, red check without metadata, and diff checks.

[christso]

Blocking review result for current head b089848a.

I re-checked the two earlier P1s and they are still present in #1460:

1. .beads/metadata.json is still deleted and .beads/.gitignore now ignores metadata.json. That removes the tracked embedded Dolt identity (dolt_database: av, project_id: a7aea826-...) rather than preserving/recovering it, so existing embedded Dolt data can still fall back to database beads / zero issues.
2. .beads/config.yaml.example only sets federation.remote. It still does not set sync.remote, and bd bootstrap explicitly keys off sync.remote first. In a disposable fresh fixture using this PR template, bd bootstrap --dry-run --json planned:
   • database: "beads"
   • sync_remote: "git+https://github.com/EntityProcess/agentv.git"
   • reason: found Dolt data on git origin, so it would clone from the code repo.

The av-21i acceptance criteria are therefore not met yet: no PR-local change/runbook covers the code-repo vs beads-repo split and recovery path, and no metadata/db mismatch guard with an actionable fix is included in this diff.

Checks run:

• git diff --check origin/main...refs/review/pr-1460-head passed.
• git ls-tree -r --name-only refs/review/pr-1460-head .beads shows only .beads/.gitignore and .beads/config.yaml.example.
• Disposable /tmp bootstrap dry-run reproduced the sync.remote/code-repo selection issue above.

CI is green and the PR remains draft, but this is not merge-ready.

[christso]

Implementation follow-up for av-21i.2 is pushed at head 59be3180.

Changes:

• Restored tracked .beads/metadata.json with AgentV embedded Dolt identity (dolt_database: av, project a7aea826-0087-45fc-93f5-9084e9924e8b).
• Removed metadata.json from .beads/.gitignore while keeping checkout-local .beads/config.yaml ignored.
• Added sync.remote to .beads/config.yaml.example so bootstrap templates select git+https://github.com/EntityProcess/agentv-beads.git instead of the public code repo.
• Added scripts/check-beads-context.ts, bun run beads:check, and docs/runbooks/beads-worktree-recovery.md with the code-repo vs Beads-repo split, recovery steps, and metadata/bootstrap mismatch fix hints.

Verification run:

• git diff --check
• git diff --check origin/main...HEAD
• bun run beads:check -- --skip-bd
• bun run beads:check -- --fixture (disposable fresh-bootstrap fixture resolved database av and bootstrap sync_remote to EntityProcess/agentv-beads)
• bun run beads:check (passed with one expected warning that this worktree uses the primary checkout Beads dir)
• bun run lint

Relevant-suite search: I did not find an existing Beads/workmux test suite beyond this guard/script path.

Remaining status: PR #1460 is still draft and should remain draft until independent re-review. Refreshed GitHub checks have started and were still pending when checked after push.

[christso]

CI update for head 59be3180: refreshed GitHub checks are green.

Passed checks:

• CI: Build, Typecheck, Lint, Test, Check Links, Validate Marketplace, Validate Evals
• Dependency Audit: Audit dependencies, Check Bun lockfile
• Cloudflare Pages

PR remains draft pending independent re-review; not merging.

[christso]

Independent post-fix review for av-21i.3 at 59be3180e7c89996955556b85bc39aae3524c15f: no blockers found.

Acceptance verification:

• Local HEAD, tracking branch origin/av-21i-beads-workmux-hardening, and GitHub PR head all resolve to 59be3180e7c89996955556b85bc39aae3524c15f.
• .beads/metadata.json is tracked, is not ignored by .beads/.gitignore, and preserves the AgentV embedded Dolt identity: database av, project a7aea826-0087-45fc-93f5-9084e9924e8b.
• .beads/config.yaml.example now pins both sync.remote and federation.remote to git+https://github.com/EntityProcess/agentv-beads.git, while checkout-local .beads/config.yaml is ignored and not tracked.
• docs/runbooks/beads-worktree-recovery.md documents the EntityProcess/agentv code repo vs EntityProcess/agentv-beads coordination repo split, fresh worktree bootstrap steps, and recovery steps for metadata/context/remote mismatches.
• scripts/check-beads-context.ts surfaces actionable fixes for metadata identity mismatch, current bd context mismatch, and bootstrap sync_remote mismatch.

Focused checks run:

• bun run beads:check -- --fixture passed: disposable fixture reported database av and bootstrap dry-run from EntityProcess/agentv-beads.
• bun run beads:check -- --skip-bd passed: static checks reported 0 errors and the expected warning that local .beads/config.yaml is missing in this review checkout.
• bun run beads:check passed: current checkout reported 0 errors, with expected warnings for missing local config and shared primary-checkout Beads context.
• git diff --check origin/main...HEAD passed.

GitHub CI status checked after review: all current checks are passing on 59be3180 (Build, Typecheck, Lint, Test, Check Links, Validate Marketplace, Validate Evals, Dependency Audit checks, and Cloudflare Pages).

I left PR #1460 draft and unmerged.