diff --git a/.beads/issues.jsonl b/.beads/issues.jsonl
index f3bf74c4..54310361 100644
--- a/.beads/issues.jsonl
+++ b/.beads/issues.jsonl
@@ -1,5 +1,6 @@
 {"id":"bd-03r","title":"Document deletions manifest in AGENTS.md and README","description":"Parent: bd-imj\n\n## Task\nAdd documentation about the deletions manifest feature.\n\n## Locations to Update\n\n### AGENTS.md\n- Explain that deletions.jsonl is tracked in git\n- Document that `bd delete` records to the manifest\n- Explain cross-clone propagation mechanism\n\n### README.md  \n- Brief mention in .beads directory structure section\n- Link to detailed docs if needed\n\n### docs/deletions.md (new file)\n- Full technical documentation\n- Format specification\n- Pruning policy\n- Git history fallback\n- Troubleshooting\n\n## Acceptance Criteria\n- AGENTS.md updated with deletion workflow\n- README.md mentions deletions.jsonl purpose\n- New docs/deletions.md with complete reference","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T14:56:49.13027-08:00","updated_at":"2025-11-25T15:17:23.145944-08:00","closed_at":"2025-11-25T15:17:23.145944-08:00"}
 {"id":"bd-055","title":"Fix hyphenated prefix parsing in ExtractIssuePrefix (GH #395)","description":"","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T15:22:22.395177-08:00","updated_at":"2025-11-26T16:46:57.8927-08:00","closed_at":"2025-11-26T16:46:57.8927-08:00"}
+{"id":"bd-0b2","title":"Need --no-git-history flag to disable git history backfill during import","description":"During JSONL migration (beads.jsonl → issues.jsonl), the git history backfill mechanism causes data loss by finding issues in the old beads.jsonl git history and incorrectly treating them as deleted.\n\nA --no-git-history flag for 'bd import' and 'bd sync' would allow users to disable the git history fallback when it's causing problems.\n\nUse cases:\n- JSONL filename migrations\n- Repos with complex git history\n- Debugging import issues\n- Performance (skip slow git scans)\n\nRelated: bd-0gh (migration causes spurious deletions)","status":"open","priority":2,"issue_type":"feature","created_at":"2025-11-26T22:28:22.5286-08:00","updated_at":"2025-11-26T22:28:22.5286-08:00"}
 {"id":"bd-1pj6","title":"Proposal: Custom status states via config","description":"Proposal to add 'custom status states' via `bd config`.\nUsers could define an optional issue status enum (e.g., awaiting_review, review_in_progress) in the config.\nThis would enable multi-step pipelines to process issues where each step correlates to a specific status.\n\nExamples:\n- awaiting_verification\n- awaiting_docs\n- awaiting_testing\n","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-20T18:55:48.670499-05:00","updated_at":"2025-11-20T18:55:48.670499-05:00"}
 {"id":"bd-2em","title":"Expand checkHooksQuick to verify all hook versions","description":"Currently checkHooksQuick only checks post-merge hook version. Should also check pre-commit, pre-push, and post-checkout for completeness. Keep it lightweight but catch more outdated hooks.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:47.432243-08:00","updated_at":"2025-11-25T19:50:21.378464-08:00","closed_at":"2025-11-25T19:50:21.378464-08:00"}
 {"id":"bd-39o","title":"Rename last_import_hash metadata key to jsonl_content_hash","description":"The metadata key 'last_import_hash' is misleading because it's updated on both import AND export (sync.go:614, import.go:320).\n\nBetter names:\n- jsonl_content_hash (more accurate)\n- last_sync_hash (clearer intent)\n\nThis is a breaking change requiring migration of existing metadata values.","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:31:07.568739-05:00","updated_at":"2025-11-20T21:31:07.568739-05:00"}
@@ -8,9 +9,12 @@
 {"id":"bd-4aao","title":"Fix failing integration tests in beads-mcp","description":"The `beads-mcp` test suite has failures in `tests/test_bd_client_integration.py` (assertion error in `test_init_creates_beads_directory`) and errors in `tests/test_worktree_separate_dbs.py` (setup failures finding database). These need to be investigated and fixed to ensure a reliable CI baseline.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:53:28.4803-05:00","updated_at":"2025-11-25T21:39:20.967106-08:00","closed_at":"2025-11-25T21:39:20.967106-08:00"}
 {"id":"bd-4h3","title":"Add test coverage for internal/git package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:23.497486-05:00","updated_at":"2025-11-20T21:21:23.497486-05:00","dependencies":[{"issue_id":"bd-4h3","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.277639-05:00","created_by":"daemon"}]}
 {"id":"bd-4l5","title":"bd prime: Detect ephemeral branches and adjust workflow output","description":"When 'bd prime' runs on a branch with no upstream (ephemeral branch), it should output a different SESSION CLOSE PROTOCOL.\n\n**Current output (wrong for ephemeral branches):**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync\n[ ] 4. git commit -m \"...\"\n[ ] 5. bd sync\n[ ] 6. git push\n```\n\n**Needed output for ephemeral branches:**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync --from-main  (pull updates from main)\n[ ] 4. git commit -m \"...\"\n[ ] 5. (no push - branch is ephemeral)\n```\n\n**Detection:** `git rev-parse --abbrev-ref --symbolic-full-name @{u}` returns error code 128 if no upstream.\n\nAlso update Sync \u0026 Collaboration section to mention `bd sync --from-main` for ephemeral branches.\n\n**Use case:** Gastown polecats work on ephemeral local branches that are never pushed. Their code gets merged to main via local merge, and beads changes stay local (communicated via gm mail to Overseer).","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-25T16:55:24.984104-08:00","updated_at":"2025-11-25T17:12:46.604978-08:00","closed_at":"2025-11-25T17:12:46.604978-08:00"}
+{"id":"bd-4pv","title":"bd export only outputs 1 issue after auto-import corrupts database","description":"When auto-import runs and purges issues (due to git history backfill bug), subsequent 'bd export' only exports 1 issue even though the database should have many.\n\nReproduction:\n1. Have issues.jsonl with 55 issues\n2. Auto-import triggers and purges all issues via git history backfill\n3. Run 'bd export' - only exports 1 issue (the last one created before corruption)\n\nThe database gets into an inconsistent state where most issues are purged but export doesn't realize this.\n\nWorkaround: Rebuild database from scratch with 'rm .beads/beads.db \u0026\u0026 bd init --prefix bd'","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:40.828866-08:00","updated_at":"2025-11-26T22:28:40.828866-08:00"}
+{"id":"bd-4t7","title":"Auto-import runs during --no-auto-import operations via stats/ready commands","description":"Even when using --no-auto-import flag, certain commands like 'bd stats' and 'bd ready' still trigger auto-import internally, which can cause the git history backfill bug to corrupt data.\n\nExample:\n  bd stats --no-auto-import\n  # Still prints 'Purged bd-xxx (recovered from git history...)'\n\nThe flag should completely disable auto-import for the command, but it appears some code paths still trigger it.\n\nWorkaround: Use --allow-stale instead, or --sandbox mode.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:59.305898-08:00","updated_at":"2025-11-26T22:28:59.305898-08:00"}
 {"id":"bd-6xd","title":"Standardize on issues.jsonl as canonical filename","description":"## Background\n\nThe codebase has confused and contradictory references to both `issues.jsonl` and `beads.jsonl`. This arose from a misconception that `issues.jsonl` was polluted with 100k test issues, but analysis shows:\n\n- issues.jsonl git history: 253 blobs, 54 MB total (max blob 2.1 MB)\n- beads.jsonl git history: 1140 blobs, 353 MB total (6.5x larger!)\n\nThe 'pollution' was never as big as remembered. Meanwhile, 99% of user installs use `issues.jsonl`.\n\n## The Problem\n\nCode has contradictory comments:\n```go\n// cmd/bd/autoimport.go:88\n// Try canonical JSONL filenames in precedence order (issues.jsonl is canonical)\n\n// internal/configfile/configfile.go:24\nJSONLExport: \"beads.jsonl\", // Default to canonical name (was issues.jsonl)\n```\n\n## Current State\n\n### Code References (excluding tests)\n- `beads.jsonl`: 51 references in Go code\n- `issues.jsonl`: 84 references in Go code\n\n### Documentation References\n- `beads.jsonl`: 59 references\n- `issues.jsonl`: 62 references\n\n## Proposed Solution\n\n1. Make `issues.jsonl` the **only** canonical name\n2. Support `beads.jsonl` only as legacy (auto-migrate to issues.jsonl)\n3. Switch beads repo itself back to using issues.jsonl\n4. Update all code and docs for consistency\n\n## Files Requiring Changes\n\n### High Priority (logic changes)\n- `internal/configfile/configfile.go` - Change default from beads.jsonl to issues.jsonl\n- `internal/beads/beads.go` - Reverse preference order, prefer issues.jsonl\n- `cmd/bd/version_tracking.go` - Reverse preference order\n- `cmd/bd/doctor/fix/database_config.go` - Reverse preference order\n- `cmd/bd/autoimport.go` - Already prefers issues.jsonl (correct)\n- `cmd/bd/init.go` - Update gitattributes setup, comments\n\n### Medium Priority (user-facing messages)\n- `cmd/bd/import.go` - Update example paths in error messages\n- `cmd/bd/sync.go` - Update diff display path\n- `cmd/bd/status.go` - Update git log path\n- `cmd/bd/staleness.go` - Update help message\n- `cmd/bd/init_contributor.go` - Update output messages\n- `cmd/bd/clean.go` - Update help text\n- `cmd/bd/cleanup.go` - Update help text\n\n### Lower Priority (internal/comments)\n- `internal/importer/importer.go` - Update comments and paths\n- `cmd/bd/merge.go` - Update comment\n- `cmd/bd/doctor.go` - Multiple references\n- `cmd/bd/doctor/fix/sync.go` - Variable naming\n- `cmd/bd/doctor/fix/deletions.go` - Path reference\n\n### Documentation\n- README.md - ~8 references to update\n- docs/DELETIONS.md\n- docs/CLI_REFERENCE.md\n- docs/ARCHITECTURE.md\n- docs/TROUBLESHOOTING.md\n- docs/PROTECTED_BRANCHES.md\n- docs/GIT_INTEGRATION.md\n- docs/MULTI_REPO_AGENTS.md\n- docs/MULTI_REPO_MIGRATION.md\n- docs/TESTING.md (acknowledges the inconsistency)\n\n## Migration Strategy\n\n1. Add migration in `bd init`: if beads.jsonl exists and issues.jsonl doesn't, rename it\n2. Update `bd doctor` to detect and offer to fix the naming\n3. Keep reading beads.jsonl as fallback for one version cycle\n4. Remove beads.jsonl fallback in future version\n\n## For Beads Repo Itself\n\n1. `git mv .beads/beads.jsonl .beads/issues.jsonl`\n2. Update .gitattributes if present\n3. Commit with clear message","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-26T19:33:34.169595-08:00","updated_at":"2025-11-26T21:00:34.038454-08:00","closed_at":"2025-11-26T21:00:34.038454-08:00"}
 {"id":"bd-736d","title":"Refactor path canonicalization into helper function","description":"The path canonicalization logic (filepath.Abs + EvalSymlinks) is duplicated in 3 places:\n- beads.go:131-137 (BEADS_DIR handling)\n- cmd/bd/main.go:446-451 (--no-db cleanup)\n- cmd/bd/nodb.go:26-31 (--no-db initialization)\n\nRefactoring suggestion:\nExtract to a helper function like:\n  func canonicalizePath(path string) string\n\nThis would:\n- Reduce code duplication\n- Make the logic easier to maintain\n- Ensure consistent behavior across all path handling\n\nRelated to bd-e16b implementation.","status":"closed","priority":3,"issue_type":"chore","created_at":"2025-11-02T18:33:47.727443-08:00","updated_at":"2025-11-25T22:27:33.738672-08:00","closed_at":"2025-11-25T22:27:33.738672-08:00"}
 {"id":"bd-81a","title":"Add programmatic tip injection API","description":"Allow tips to be programmatically injected at runtime based on detected conditions. This enables dynamic tips (not just pre-defined ones) to be shown with custom priority and frequency.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-11T23:29:46.645583-08:00","updated_at":"2025-11-25T17:52:35.096882-08:00","closed_at":"2025-11-25T17:52:35.096882-08:00","dependencies":[{"issue_id":"bd-81a","depends_on_id":"bd-d4i","type":"blocks","created_at":"2025-11-11T23:29:46.646327-08:00","created_by":"daemon"}]}
+{"id":"bd-8an","title":"bd import auto-detects wrong prefix from directory name instead of issue IDs","description":"When importing issues.jsonl into a fresh database, 'bd import' prints:\n\n  ✓ Initialized database with prefix 'beads' (detected from issues)\n\nBut the issues all have prefix 'bd-' (e.g., bd-03r). It appears to be detecting the prefix from the directory name (.beads/) rather than from the actual issue IDs in the JSONL.\n\nThis causes import to fail with:\n  validate ID prefix for bd-03r: issue ID 'bd-03r' does not match configured prefix 'beads'\n\nWorkaround: Run 'bd config set issue_prefix bd' before import, or use 'bd init --prefix bd'.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:01.582564-08:00","updated_at":"2025-11-26T22:28:01.582564-08:00"}
 {"id":"bd-9e23","title":"Optimize Memory backend GetIssueByExternalRef with index","description":"Currently GetIssueByExternalRef in Memory storage uses O(n) linear search through all issues.\n\nCurrent code (memory.go:282-308):\nfor _, issue := range m.issues {\n    if issue.ExternalRef != nil \u0026\u0026 *issue.ExternalRef == externalRef {\n        return \u0026issueCopy, nil\n    }\n}\n\nProposed optimization:\n- Add externalRefToID map[string]string to MemoryStorage\n- Maintain it in CreateIssue, UpdateIssue, DeleteIssue\n- Achieve O(1) lookup like SQLite's index\n\nImpact: Low (--no-db mode typically has smaller datasets)\nRelated: bd-1022","status":"closed","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:30.242357-08:00","updated_at":"2025-11-26T11:14:49.172418-08:00","closed_at":"2025-11-26T11:14:49.172418-08:00"}
 {"id":"bd-9li4","title":"Create Docker image for Agent Mail","description":"Containerize Agent Mail server for easy deployment.\n\nAcceptance Criteria:\n- Dockerfile with Python 3.14\n- Health check endpoint\n- Volume mount for storage\n- Environment variable configuration\n- Multi-arch builds (amd64, arm64)\n\nFile: deployment/agent-mail/Dockerfile","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-07T22:43:43.231964-08:00","updated_at":"2025-11-25T17:47:30.777486-08:00","closed_at":"2025-11-25T17:47:30.777486-08:00"}
 {"id":"bd-b8h","title":"Refactor check-health DB access to avoid repeated path resolution","description":"The runCheckHealth lightweight checks (hintsDisabled, checkVersionMismatch, checkSyncBranchQuick) each have duplicated database path resolution logic. Extract a helper function to DRY this up.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:35.075929-08:00","updated_at":"2025-11-25T19:50:21.272961-08:00","closed_at":"2025-11-25T19:50:21.272961-08:00"}
@@ -20,7 +24,7 @@
 {"id":"bd-c362","title":"Extract database search logic into helper function","description":"The logic for finding a database in a beads directory is duplicated:\n- FindDatabasePath() BEADS_DIR section (beads.go:141-169)\n- findDatabaseInTree() (beads.go:248-280)\n\nBoth implement the same search order:\n1. Check config.json first (single source of truth)\n2. Fall back to canonical beads.db\n3. Search for *.db files, filtering backups and vc.db\n\nRefactoring suggestion:\nExtract to a helper function like:\n  func findDatabaseInBeadsDir(beadsDir string) string\n\nBenefits:\n- Single source of truth for database search logic\n- Easier to maintain and update search order\n- Reduces code duplication\n\nRelated to [deleted:bd-e16b] implementation.","status":"closed","priority":3,"issue_type":"chore","created_at":"2025-11-02T18:34:02.831543-08:00","updated_at":"2025-11-25T22:27:33.794656-08:00","closed_at":"2025-11-25T22:27:33.794656-08:00"}
 {"id":"bd-c4rq","title":"Refactor: Move staleness check inside daemon branch","description":"## Problem\n\nCurrently ensureDatabaseFresh() is called before the daemon mode check, but it checks daemonClient != nil internally and returns early. This is redundant.\n\n**Location:** All read commands (list.go:196, show.go:27, ready.go:102, status.go:80, etc.)\n\n## Current Pattern\n\nCall happens before daemon check, function checks daemonClient internally.\n\n## Better Pattern\n\nMove staleness check to direct mode branch only, after daemon check.\n\n## Impact\nLow - minor performance improvement (avoids one function call per command in daemon mode)\n\n## Effort\nMedium - requires refactoring 8 command files\n\n## Priority\nLow - can defer to future cleanup PR","status":"open","priority":3,"issue_type":"chore","created_at":"2025-11-20T20:17:45.119583-05:00","updated_at":"2025-11-20T20:17:45.119583-05:00"}
 {"id":"bd-d4i","title":"Create tip system infrastructure for contextual hints","description":"Implement a tip/hint system that shows helpful contextual messages after successful commands. This is different from the existing error-path \"Hint:\" messages - tips appear on success paths to educate users about features they might not know about.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-11T23:29:15.693956-08:00","updated_at":"2025-11-25T17:47:30.747566-08:00","closed_at":"2025-11-25T17:47:30.747566-08:00"}
-{"id":"bd-e166","title":"Improve timestamp comparison readability in import","description":"The timestamp comparison logic uses double-negative which can be confusing:\n\nCurrent code:\nif !incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // skip update\n}\n\nMore readable:\nif incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // perform update\n} else {\n    // skip (local is newer)\n}\n\nThis is a minor refactor for code clarity.\n\nRelated: bd-1022\nFiles: internal/importer/importer.go:411, 488","status":"open","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:12.27108-08:00","updated_at":"2025-11-02T15:32:12.27108-08:00"}
+{"id":"bd-e166","title":"Improve timestamp comparison readability in import","description":"The timestamp comparison logic uses double-negative which can be confusing:\n\nCurrent code:\nif !incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // skip update\n}\n\nMore readable:\nif incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // perform update\n} else {\n    // skip (local is newer)\n}\n\nThis is a minor refactor for code clarity.\n\nRelated: bd-1022\nFiles: internal/importer/importer.go:411, 488","status":"closed","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:12.27108-08:00","updated_at":"2025-11-26T22:25:27.124071-08:00","closed_at":"2025-11-26T22:25:27.124071-08:00"}
 {"id":"bd-e92","title":"Add test coverage for internal/autoimport package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.338577-05:00","updated_at":"2025-11-20T21:21:22.338577-05:00","dependencies":[{"issue_id":"bd-e92","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.128625-05:00","created_by":"daemon"}]}
 {"id":"bd-f0n","title":"Git history fallback missing timeout - could hang on large repos","description":"## Problem\n\nThe git commands in `checkGitHistoryForDeletions` have no timeout. On large repos with extensive history, `git log --all -S` or `git log --all -G` can take a very long time (minutes).\n\n## Location\n`internal/importer/importer.go:899` and `:930`\n\n## Impact\n- Import could hang indefinitely\n- User has no feedback that git search is running\n- No way to cancel except killing the process\n\n## Fix\nAdd context with timeout to git commands:\n\n```go\nctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)\ndefer cancel()\ncmd := exec.CommandContext(ctx, \"git\", ...)\n```\n\nAlso consider adding a `--since` flag to bound the git history search.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:48:24.388639-08:00","updated_at":"2025-11-25T15:04:53.669714-08:00","closed_at":"2025-11-25T15:04:53.669714-08:00"}
 {"id":"bd-ge7","title":"Improve Beads test coverage from 46% to 80%","description":"","status":"open","priority":1,"issue_type":"epic","created_at":"2025-11-20T21:21:03.700271-05:00","updated_at":"2025-11-20T21:21:03.700271-05:00"}
@@ -35,8 +39,8 @@
 {"id":"bd-m7ge","title":"Add .beads/README.md during 'bd init' for project documentation and promotion","description":"When 'bd init' is run, automatically generate a .beads/README.md file that:\n\n1. Briefly explains what Beads is (AI-native issue tracking that lives in your repo)\n2. Links to the main repository: https://github.com/steveyegge/beads\n3. Provides a quick reference of essential commands:\n   - bd create: Create new issues\n   - bd list: View all issues\n   - bd update: Modify issue status/details\n   - bd show: View issue details\n   - bd sync: Sync with git remote\n4. Highlights key benefits for AI coding agents and developers\n5. Encourages developers to try it out\n\nThe README should be enthusiastic and compelling to get open source contributors excited about using Beads for their AI-assisted development workflows.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-16T22:32:50.478681-08:00","updated_at":"2025-11-25T17:49:42.558381-08:00","closed_at":"2025-11-25T17:49:42.558381-08:00"}
 {"id":"bd-mdw","title":"Add integration test for cross-clone deletion propagation","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T14:56:38.997009-08:00","updated_at":"2025-11-25T16:35:59.052914-08:00","closed_at":"2025-11-25T16:35:59.052914-08:00"}
 {"id":"bd-mnap","title":"Investigate performance issues in VS Code Copilot (Windows)","description":"Beads unusable in Windows 11 VS Code Copilot chat with Sonnet 4.5.\nSummary event happens every 3-4 turns, taking 3 minutes.\nCopilot summarizes after ~125k tokens despite model supporting 1M.\nLarge context size of beads might be triggering aggressive summarization.\nNeed workaround or optimization for context size.\n","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:30.124918-05:00","updated_at":"2025-11-20T18:56:30.124918-05:00"}
-{"id":"bd-nq41","title":"Fix Homebrew warning about Ruby file location","description":"Homebrew warning: Found Ruby file outside steveyegge/beads tap formula directory.\nWarning points to: /opt/homebrew/Library/Taps/steveyegge/homebrew-beads/bd.rb\nIt should likely be inside a Formula/ directory or similar structure expected by Homebrew taps.\n","status":"open","priority":2,"issue_type":"chore","created_at":"2025-11-20T18:56:21.226579-05:00","updated_at":"2025-11-20T18:56:21.226579-05:00"}
-{"id":"bd-p6vp","title":"Clarify .beads/.gitattributes handling in Protected Branches docs","description":"Protected Branches docs quick start leaves untracked `.beads` directory and `.gitattributes`.\nQuestion: Are these changes meant to be checked into the protected branch?\nNeed to clarify if these should be ignored or committed, or if the instructions are missing a step.\n","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:25.79407-05:00","updated_at":"2025-11-20T18:56:25.79407-05:00"}
+{"id":"bd-nq41","title":"Fix Homebrew warning about Ruby file location","description":"Homebrew warning: Found Ruby file outside steveyegge/beads tap formula directory.\nWarning points to: /opt/homebrew/Library/Taps/steveyegge/homebrew-beads/bd.rb\nIt should likely be inside a Formula/ directory or similar structure expected by Homebrew taps.\n","status":"closed","priority":2,"issue_type":"chore","created_at":"2025-11-20T18:56:21.226579-05:00","updated_at":"2025-11-26T22:25:37.362928-08:00","closed_at":"2025-11-26T22:25:37.362928-08:00"}
+{"id":"bd-p6vp","title":"Clarify .beads/.gitattributes handling in Protected Branches docs","description":"Protected Branches docs quick start leaves untracked `.beads` directory and `.gitattributes`.\nQuestion: Are these changes meant to be checked into the protected branch?\nNeed to clarify if these should be ignored or committed, or if the instructions are missing a step.\n","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:25.79407-05:00","updated_at":"2025-11-26T22:25:47.574326-08:00","closed_at":"2025-11-26T22:25:47.574326-08:00"}
 {"id":"bd-pbj","title":"bd doctor --fix should run bd sync to commit untracked deletions.jsonl","description":"After running bd cleanup -f, the deletions.jsonl file is created but left untracked. bd doctor --fix should notice this and run bd sync to commit it.\n\nCurrent behavior:\n- bd cleanup -f creates/updates deletions.jsonl\n- git status shows deletions.jsonl as untracked\n- bd doctor --fix does not notice or fix this\n\nExpected behavior:\n- bd doctor --fix should detect untracked .beads/*.jsonl files\n- Should offer to run bd sync to commit them\n\nRelated: The git hooks were also missing deletions.jsonl from their staging loops - that's been fixed in this session.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T20:29:33.901199-08:00","updated_at":"2025-11-26T20:33:03.296592-08:00","closed_at":"2025-11-26T20:33:03.296592-08:00"}
 {"id":"bd-qsm","title":"Auto-compact deletions during bd sync","description":"Parent: bd-imj\n\n## Task\nOptionally prune deletions manifest during sync when threshold exceeded.\n\n**Note: Opt-in feature** - disabled by default to avoid sync latency.\n\n## Implementation\n\nIn `bd sync`:\n```go\nfunc (s *Syncer) Sync() error {\n    // ... existing sync logic ...\n    \n    // Auto-compact only if enabled\n    if s.config.GetBool(\"deletions.auto_compact\", false) {\n        deletionCount := deletions.Count(\".beads/deletions.jsonl\")\n        threshold := s.config.GetInt(\"deletions.auto_compact_threshold\", 1000)\n        \n        if deletionCount \u003e threshold {\n            retentionDays := s.config.GetInt(\"deletions.retention_days\", 7)\n            if err := s.compactor.PruneDeletions(retentionDays); err != nil {\n                log.Warnf(\"Failed to auto-compact deletions: %v\", err)\n                // Non-fatal, continue sync\n            }\n        }\n    }\n    \n    // ... rest of sync ...\n}\n```\n\n## Configuration\n```yaml\ndeletions:\n  retention_days: 7\n  auto_compact: false              # Opt-in, disabled by default\n  auto_compact_threshold: 1000     # Trigger when \u003e N entries (if enabled)\n```\n\n## Acceptance Criteria\n- [ ] Auto-compact disabled by default\n- [ ] Enabled via config `deletions.auto_compact: true`\n- [ ] Sync checks deletion count only when enabled\n- [ ] Auto-prunes when threshold exceeded\n- [ ] Failure is non-fatal (logged warning)\n- [ ] Test: no compaction when disabled\n- [ ] Test: compaction triggers when enabled and threshold exceeded","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-25T09:57:04.522795-08:00","updated_at":"2025-11-25T15:03:01.469629-08:00","closed_at":"2025-11-25T15:03:01.469629-08:00"}
 {"id":"bd-red","title":"bd sync should only commit .beads/ files, not all staged changes","description":"Currently bd sync commits ALL staged files, not just .beads/*.jsonl. This can lead to:\n- Unintended commits of work-in-progress code\n- Surprise for users/agents who staged files but weren't ready to commit\n- Mixing beads sync commits with actual code changes\n\nExpected behavior: bd sync should only stage and commit .beads/ files, leaving other staged changes alone.\n\nOptions:\n1. Stash other staged changes, commit only .beads/, restore stash\n2. Use git add .beads/ \u0026\u0026 git commit -m '...' -- .beads/ to only commit beads files\n3. Warn if non-beads files are staged and require --force to proceed","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T20:35:40.212006-08:00","updated_at":"2025-11-26T20:46:26.106545-08:00","closed_at":"2025-11-26T20:46:26.106545-08:00"}
@@ -50,6 +54,7 @@
 {"id":"bd-wmo","title":"PruneDeletions iterates map non-deterministically","description":"## Problem\n\n`PruneDeletions` iterates over `loadResult.Records` which is a map. Go maps iterate in random order, so:\n\n1. `result.PrunedIDs` order is non-deterministic\n2. `kept` slice order is non-deterministic → `WriteDeletions` output order varies\n\n## Location\n`internal/deletions/deletions.go:213`\n\n## Impact\n- Git diffs are noisy (file changes order on each prune)\n- Tests could be flaky if they depend on order\n- Harder to debug/audit\n\n## Fix\nSort by ID or timestamp before iterating:\n\n```go\n// Convert map to slice and sort\nvar records []DeletionRecord\nfor _, r := range loadResult.Records {\n    records = append(records, r)\n}\nsort.Slice(records, func(i, j int) bool {\n    return records[i].ID \u003c records[j].ID\n})\n```","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-11-25T12:49:11.290916-08:00","updated_at":"2025-11-25T15:15:21.903649-08:00","closed_at":"2025-11-25T15:15:21.903649-08:00"}
 {"id":"bd-x2i","title":"Add bd deleted command for audit trail","description":"Parent: bd-imj\n\nAdd command to view deletion history.\n\nUsage:\n  bd deleted              # Show recent deletions (last 7 days)\n  bd deleted --since=30d  # Show deletions in last 30 days\n  bd deleted --all        # Show all tracked deletions\n  bd deleted bd-xxx       # Show deletion details for specific issue\n\nOutput format:\n  bd-xxx  2025-11-25 10:00  stevey  duplicate of bd-yyy\n  bd-yyy  2025-11-25 10:05  claude  cleanup\n\nAcceptance criteria:\n- List deletions with timestamp, actor, reason\n- Filter by time range\n- Lookup specific issue ID\n- JSON output option for scripting","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T09:57:21.113861-08:00","updated_at":"2025-11-25T15:13:53.781519-08:00","closed_at":"2025-11-25T15:13:53.781519-08:00"}
 {"id":"bd-xyc","title":"Consolidate check-health DB opens into single connection","description":"The --check-health flag opens the database 3 separate times (once per quick check). Consolidate into a single DB open for better performance, especially on slower filesystems.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:42.034178-08:00","updated_at":"2025-11-25T19:50:21.32375-08:00","closed_at":"2025-11-25T19:50:21.32375-08:00"}
-{"id":"bd-ybv5","title":"Refactor AGENTS.md to use external references","description":"Suggestion to use external references (e.g., \"ALWAYS REFER TO ./beads/prompt.md\") instead of including all instructions directly within AGENTS.md.\nReasons:\n1. Agents can follow external references.\n2. Prevents context pollution/stuffing in AGENTS.md as more tools append instructions.\n","status":"open","priority":3,"issue_type":"task","created_at":"2025-11-20T18:55:53.259144-05:00","updated_at":"2025-11-20T18:55:53.259144-05:00"}
+{"id":"bd-ybv5","title":"Refactor AGENTS.md to use external references","description":"Suggestion to use external references (e.g., \"ALWAYS REFER TO ./beads/prompt.md\") instead of including all instructions directly within AGENTS.md.\nReasons:\n1. Agents can follow external references.\n2. Prevents context pollution/stuffing in AGENTS.md as more tools append instructions.\n","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-20T18:55:53.259144-05:00","updated_at":"2025-11-26T22:25:57.772875-08:00","closed_at":"2025-11-26T22:25:57.772875-08:00"}
 {"id":"bd-ye0d","title":"troubleshoot GH#278 daemon exits every few secs","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-13T06:27:23.39509215-07:00","updated_at":"2025-11-25T17:48:43.62418-08:00","closed_at":"2025-11-25T17:48:43.62418-08:00"}
+{"id":"bd-zai","title":"bd init resets metadata.json jsonl_export to beads.jsonl, ignoring existing issues.jsonl","description":"When running 'bd init --prefix bd' in a repo that already has .beads/issues.jsonl, the init command overwrites metadata.json and sets jsonl_export back to 'beads.jsonl' instead of detecting and respecting the existing issues.jsonl file.\n\nSteps to reproduce:\n1. Have a repo with .beads/issues.jsonl (canonical) and metadata.json pointing to issues.jsonl\n2. Delete beads.db and run 'bd init --prefix bd'\n3. Check metadata.json - it now says jsonl_export: beads.jsonl\n\nExpected: Init should detect existing issues.jsonl and use it.\n\nWorkaround: Manually edit metadata.json after init.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:27:41.653287-08:00","updated_at":"2025-11-26T22:27:41.653287-08:00"}
 {"id":"bd-zj8e","title":"Performance Testing Documentation","description":"Create docs/performance-testing.md documenting the performance testing framework.\n\nSections:\n1. Overview - What the framework does, goals\n2. Running Benchmarks\n   - make bench command\n   - Running specific benchmarks\n   - Interpreting output (ns/op, allocs/op)\n3. Profiling and Analysis\n   - Viewing CPU profiles with pprof\n   - Reading flamegraphs\n   - Memory profiling\n   - Finding hotspots\n4. User Diagnostics\n   - bd doctor --perf usage\n   - Sharing profiles with bug reports\n   - Understanding the report output\n5. Comparing Performance\n   - Using benchstat for before/after comparisons\n   - Detecting regressions\n6. Tips for Optimization\n   - Common patterns\n   - When to profile vs benchmark\n\nStyle:\n- Concise, practical examples\n- Screenshots/examples of pprof output\n- Clear command-line examples\n- Focus on workflow, not theory","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-13T22:23:38.99897-08:00","updated_at":"2025-11-13T22:23:38.99897-08:00"}