chore: bd doctor --fix and sync

.beads/.gitignore

@@ -10,11 +10,20 @@ daemon.lock
 daemon.log
 daemon.pid
 bd.sock
+sync-state.json
+last-touched
+
+# Local version tracking (prevents upgrade notification spam after git ops)
+.local_version
 
 # Legacy database files
 db.sqlite
 bd.db
 
+# Worktree redirect file (contains relative path to main repo's .beads/)
+# Must not be committed as paths would be wrong in other clones
+redirect
+
 # Merge artifacts (temporary files from 3-way merge)
 beads.base.jsonl
 beads.base.meta.json
@@ -23,7 +32,8 @@ beads.left.meta.json
 beads.right.jsonl
 beads.right.meta.json
 
-# Keep JSONL exports and config (source of truth for git)
-!issues.jsonl
-!metadata.json
-!config.json
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
+# They would override fork protection in .git/info/exclude, allowing
+# contributors to accidentally commit upstream issue databases.
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
+# are tracked by git by default since no pattern above ignores them.

.beads/.local_version

@@ -1 +1 @@
-0.42.0
+0.43.0

.beads/issues.jsonl

@@ -111,7 +111,7 @@
 {"id":"skills-r5c","title":"Extract shared logging library from scripts","description":"Duplicated logging/color functions across multiple scripts:\n- bin/deploy-skill.sh\n- skills/tufte-press/scripts/generate-and-build.sh\n- Other .specify scripts\n\nPattern repeated:\n- info(), warn(), error() functions\n- Color definitions (RED, GREEN, etc.)\n- Same 15-20 lines in each file\n\nFix:\n- Create scripts/common-logging.sh\n- Source from all scripts that need it\n- Estimated reduction: 30+ lines of duplication\n\nSeverity: MEDIUM","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-24T02:50:58.324852578-05:00","updated_at":"2025-12-29T18:48:20.448077879-05:00","closed_at":"2025-12-29T18:48:20.448077879-05:00","close_reason":"Minimal duplication: only 2 files with different logging styles. Shared library overhead not justified."}
 {"id":"skills-rex","title":"Test integration on worklog skill","description":"Use worklog skill as first real test case:\n- Create wisp for worklog execution\n- Capture execution trace\n- Test squash → digest\n- Validate trace format captures enough info for replay\n\nMigrated from dotfiles-drs.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-23T19:21:18.75525644-05:00","updated_at":"2025-12-29T13:55:35.814174815-05:00","closed_at":"2025-12-29T13:55:35.814174815-05:00","close_reason":"Parked with ADR-001: skills-molecules integration deferred. Current simpler approach (skills as standalone) works well. Revisit when complex orchestration needed.","dependencies":[{"issue_id":"skills-rex","depends_on_id":"skills-3em","type":"blocks","created_at":"2025-12-23T19:22:00.34922734-05:00","created_by":"dan"}]}
 {"id":"skills-rpf","title":"Implement playwright-visit skill for browser automation","description":"## Overview\nBrowser automation skill using Playwright to visit web pages, take screenshots, and extract content.\n\n## Key Findings (from dotfiles investigation)\n\n### Working Setup\n- Use `python312Packages.playwright` from nixpkgs (handles Node driver binary patching for NixOS)\n- Use `executable_path='/run/current-system/sw/bin/chromium'` to use system chromium\n- No `playwright install` needed - no browser binary downloads\n\n### Profile Behavior\n- Fresh/blank profile every launch by default\n- No cookies, history, or logins from user's browser\n- Can persist state with `storage_state` parameter if needed\n\n### Example Code\n```python\nfrom playwright.sync_api import sync_playwright\n\nwith sync_playwright() as p:\n    browser = p.chromium.launch(\n        executable_path='/run/current-system/sw/bin/chromium',\n        headless=True\n    )\n    page = browser.new_page()\n    page.goto('https://example.com')\n    print(page.title())\n    browser.close()\n```\n\n### Why Not uv/pip?\n- Playwright pip package bundles a Node.js driver binary\n- NixOS can't run dynamically linked executables without patching\n- nixpkgs playwright handles this properly\n\n## Implementation Plan\n1. Create `skills/playwright-visit/` directory\n2. Add flake.nix with devShell providing playwright\n3. Create CLI script with subcommands:\n   - `screenshot \u003curl\u003e \u003coutput.png\u003e` - capture page\n   - `text \u003curl\u003e` - extract text content  \n   - `html \u003curl\u003e` - get rendered HTML\n   - `pdf \u003curl\u003e \u003coutput.pdf\u003e` - save as PDF\n4. Create skill definition for Claude Code integration\n5. Document usage in skill README\n\n## Dependencies\n- nixpkgs python312Packages.playwright\n- System chromium (already in dotfiles)\n\n## Related\n- dotfiles issue dotfiles-m09 (playwright skill request)","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-12-16T16:02:28.577381007-08:00","updated_at":"2025-12-29T00:09:50.681141882-05:00","closed_at":"2025-12-29T00:09:50.681141882-05:00","close_reason":"Implemented: SKILL.md, visit.py CLI (screenshot/text/html/pdf), flake.nix devShell, README. Network down so couldn't test devShell build, but code complete."}
-{"id":"skills-s92","title":"Add tests for config injection (deploy-skill.sh)","description":"File: bin/deploy-skill.sh (lines 112-137)\n\nCritical logic with NO test coverage:\n- Idempotency (running twice should be safe)\n- Correct brace matching in Nix\n- Syntax validity of injected config\n- Rollback on failure\n\nRisk: MEDIUM-HIGH - can break dotfiles Nix config\n\nFix:\n- Test idempotent injection\n- Validate Nix syntax after injection\n- Test with malformed input\n\nSeverity: MEDIUM","status":"open","priority":3,"issue_type":"task","created_at":"2025-12-24T02:51:01.314513824-05:00","updated_at":"2025-12-24T02:51:01.314513824-05:00"}
+{"id":"skills-s92","title":"Add tests for config injection (deploy-skill.sh)","description":"File: bin/deploy-skill.sh (lines 112-137)\n\nCritical logic with NO test coverage:\n- Idempotency (running twice should be safe)\n- Correct brace matching in Nix\n- Syntax validity of injected config\n- Rollback on failure\n\nRisk: MEDIUM-HIGH - can break dotfiles Nix config\n\nFix:\n- Test idempotent injection\n- Validate Nix syntax after injection\n- Test with malformed input\n\nSeverity: MEDIUM","status":"in_progress","priority":3,"issue_type":"task","created_at":"2025-12-24T02:51:01.314513824-05:00","updated_at":"2026-01-02T06:15:45.352802681-05:00"}
 {"id":"skills-ty7","title":"Define trace levels (audit vs debug)","description":"Two trace levels to manage noise vs utility:\n\n1. Audit trace (minimal, safe, always on):\n   - skill id/ref, start/end\n   - high-level checkpoints\n   - artifact hashes/paths\n   - exit status\n\n2. Debug trace (opt-in, verbose):\n   - tool calls with args\n   - stdout/stderr snippets\n   - expanded inputs\n   - timing details\n\nConsider OpenTelemetry span model as reference.\nGPT proposed this; Gemini focused on rotation/caps instead.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-23T19:49:48.514684945-05:00","updated_at":"2025-12-29T13:55:35.838961236-05:00","closed_at":"2025-12-29T13:55:35.838961236-05:00","close_reason":"Parked with ADR-001: skills-molecules integration deferred. Current simpler approach (skills as standalone) works well. Revisit when complex orchestration needed."}
 {"id":"skills-u3d","title":"Define skill trigger conditions","description":"How does an agent know WHEN to apply a skill/checklist?\n\nOptions:\n- frontmatter triggers: field with patterns\n- File-based detection\n- Agent judgment from description\n- Beads hooks on state transitions\n- LLM-based pattern detection","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-23T17:59:09.69468767-05:00","updated_at":"2025-12-28T22:25:38.579989006-05:00","closed_at":"2025-12-28T22:25:38.579989006-05:00","close_reason":"Resolved: agent judgment from description is the standard. Good descriptions + 'When to Use' sections are sufficient. No new trigger mechanism needed - would add complexity without clear benefit."}
 {"id":"skills-uan","title":"worklog: merge Guidelines and Remember sections","description":"Guidelines (8 points) and Remember (6 points) sections overlap significantly - both emphasize comprehensiveness, future context, semantic compression. Consolidate into single principles list. Found by bloat lens review.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-25T02:03:16.148596791-05:00","updated_at":"2025-12-27T10:05:51.527595332-05:00","closed_at":"2025-12-27T10:05:51.527595332-05:00","close_reason":"Closed"}

.beads/last-touched

@@ -1 +1 @@
-skills-hgm
+skills-pdg