diff --git a/.beads/beads.jsonl b/.beads/beads.jsonl
index eeb0c165..6835cbd6 100644
--- a/.beads/beads.jsonl
+++ b/.beads/beads.jsonl
@@ -92,7 +92,7 @@
 {"id":"bd-5b6e","content_hash":"f82a86b4aae21311f23c8511a242f16e96d03836300995fadd43b8bea945cefa","title":"Add tests for helper functions (GetDirtyIssueHash, GetAllDependencyRecords, export hashes)","description":"Several utility functions have 0% coverage:\n- GetDirtyIssueHash (dirty.go)\n- GetAllDependencyRecords (dependencies.go)\n- GetExportHash, SetExportHash, ClearAllExportHashes (hash.go)\n\nThese are lower priority but should have basic coverage.","status":"open","priority":4,"issue_type":"task","created_at":"2025-11-01T22:40:58.989976-07:00","updated_at":"2025-11-01T22:40:58.989976-07:00"}
 {"id":"bd-5bbf","content_hash":"c5df41b585c9330b46616db9cd6d9d43650f8b4e6c6682d05caf4e450cef9192","title":"Test all core bd commands in WASM for feature parity","description":"Comprehensive testing of bd-wasm against native bd:\n- Test all CRUD operations (create, update, show, close)\n- Test dependency management (dep add, dep tree)\n- Test sync operations (sync, import, export)\n- Verify JSONL output matches native bd\n- Run existing Go test suite in WASM if possible\n- Benchmark performance (should be within 2x of native)","status":"open","priority":1,"issue_type":"task","created_at":"2025-11-02T21:58:07.300923-08:00","updated_at":"2025-11-02T21:58:07.300923-08:00","dependencies":[{"issue_id":"bd-5bbf","depends_on_id":"bd-44d0","type":"parent-child","created_at":"2025-11-02T22:23:49.503229-08:00","created_by":"stevey"},{"issue_id":"bd-5bbf","depends_on_id":"bd-b4b0","type":"blocks","created_at":"2025-11-02T22:23:55.623601-08:00","created_by":"stevey"}]}
 {"id":"bd-5ce8","content_hash":"23d02fea82e0a87bbb4c878472a368e093262e98c7d1f286374955a5b14ae1e5","title":"Document protected branch workflow","description":"Create comprehensive documentation for protected branch workflow.\n\nTasks:\n- Add \"Protected Branch Workflow\" section to AGENTS.md\n- Create docs/PROTECTED_BRANCHES.md guide\n- Update README.md quick start\n- Add examples to examples/protected-branch/\n- Update bd init --help documentation\n- Add troubleshooting guide\n- Add migration guide for existing users\n- Record demo video (optional)\n\nEstimated effort: 2-3 days","acceptance_criteria":"- Clear quick start (\u003c 2 minutes to set up)\n- Detailed guide covers all scenarios\n- Examples work end-to-end\n- Troubleshooting answers common questions\n- Platform-agnostic (not GitHub-specific)","notes":"Completed protected branch workflow documentation. Created comprehensive guide (docs/PROTECTED_BRANCHES.md), updated AGENTS.md with workflow section, added feature to README.md, and created working example (examples/protected-branch/). All commands verified working (bd init --branch, bd sync --status, bd sync --merge, bd config get/set sync.branch).","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-02T15:22:35.59013-08:00","updated_at":"2025-11-02T18:44:12.433622-08:00","closed_at":"2025-11-02T18:44:12.433625-08:00","dependencies":[{"issue_id":"bd-5ce8","depends_on_id":"bd-a101","type":"parent-child","created_at":"2025-11-02T15:22:48.379767-08:00","created_by":"stevey"}]}
-{"id":"bd-5cny","content_hash":"9cf7ac919fc45144d2b8b1ece9f92f28933d28c18679b88e37af8104404387fa","title":"Fix config.yaml no-db mode not being respected by subsequent commands","description":"GH #210: bd init --no-db creates config.yaml with no-db: false (should be true), and subsequent commands don't read this setting. Users must pass --no-db on every command.","status":"open","priority":1,"issue_type":"bug","created_at":"2025-11-03T14:58:30.565901-08:00","updated_at":"2025-11-03T14:58:30.565901-08:00"}
+{"id":"bd-5cny","content_hash":"9cf7ac919fc45144d2b8b1ece9f92f28933d28c18679b88e37af8104404387fa","title":"Fix config.yaml no-db mode not being respected by subsequent commands","description":"GH #210: bd init --no-db creates config.yaml with no-db: false (should be true), and subsequent commands don't read this setting. Users must pass --no-db on every command.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-03T14:58:30.565901-08:00","updated_at":"2025-11-03T15:01:52.774705-08:00","closed_at":"2025-11-03T15:01:52.774705-08:00"}
 {"id":"bd-5cwv","content_hash":"db14ee1a441a3684363407e0693a21627b2a98b596860dcd0a64aec969e3a964","title":"Testing base36 in beads repo with bd prefix","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-03T11:20:08.582718-08:00","updated_at":"2025-11-03T11:20:08.582718-08:00"}
 {"id":"bd-5dae5504","content_hash":"4f2b5a203d6a7b5e38176dd6ef68afb4b7d0e11889718381e28bf006f4e83a16","title":"Export deduplication breaks when JSONL and export_hashes table diverge","description":"## Problem\n\nThe export deduplication feature (timestamp-only skipping) breaks when the JSONL file and export_hashes table get out of sync, causing exports to skip issues that aren't actually in the file.\n\n## Symptoms\n\n- `bd export` reports \"Skipped 128 issue(s) with timestamp-only changes\"\n- JSONL file only has 38 lines but DB has 149 issues\n- export_hashes table has 149 entries\n- Auto-import doesn't trigger (hash matches despite missing data)\n- Two repos on same commit show different issue counts\n\n## Root Cause\n\nshouldSkipExport() in autoflush.go compares current issue hash with stored export_hashes entry. If they match, it skips export assuming the issue is already in the JSONL.\n\nThis assumption fails when:\n1. Git operations (pull, reset, checkout) change JSONL without clearing export_hashes\n2. Manual JSONL edits or corruption\n3. Import operations that modify DB but don't update export_hashes\n4. Partial exports that update export_hashes but don't complete\n\n## Impact\n\n- **Critical data loss risk**: Issues appear to be tracked but aren't persisted to git\n- Breaks multi-repo sync (root cause of today's debugging session)\n- Auto-import fails to detect staleness (hash matches despite missing data)\n- Silent data corruption (no error messages, just missing issues)\n\n## Reproduction\n\n1. Have DB with 149 issues, all in export_hashes table\n2. Truncate JSONL to 38 lines (simulate git reset or corruption)\n3. Run `bd export` - it skips 128 issues\n4. JSONL still has only 38 lines but export thinks it succeeded\n\n## Current Workaround\n\n```bash\nsqlite3 .beads/beads.db \"DELETE FROM export_hashes\"\nbd export -o .beads/beads.jsonl\n```\n\n## Proposed Solutions\n\n**Option 1: Verify JSONL integrity before skipping**\n- Count lines in JSONL, compare with export_hashes count\n- If mismatch, clear export_hashes and force full export\n- Safe but adds I/O overhead\n\n**Option 2: Hash-based JSONL validation**\n- Store hash of entire JSONL file in metadata\n- Before export, check if JSONL hash matches\n- If mismatch, clear export_hashes\n- More efficient, detects any JSONL corruption\n\n**Option 3: Disable timestamp-only deduplication**\n- Remove the feature entirely\n- Always export all issues\n- Simplest and safest, but creates larger git commits\n\n**Option 4: Clear export_hashes on git operations**\n- Add post-merge hook to clear export_hashes\n- Clear on any import operation\n- Defensive approach but may over-clear\n\n## Recommended Fix\n\nCombination of Options 2 + 4:\n1. Store JSONL file hash in metadata after export\n2. Check hash before export, clear export_hashes if mismatch  \n3. Clear export_hashes on import operations\n4. Add `bd validate` check for JSONL/export_hashes sync\n\n## Files Involved\n\n- cmd/bd/autoflush.go (shouldSkipExport)\n- cmd/bd/export.go (export with deduplication)\n- internal/storage/sqlite/metadata.go (export_hashes table)","notes":"## Recovery Session (2025-10-29 21:30)\n\n### What Happened\n- Created 14 new hash ID issues (bd-f8b764c9 through bd-f8b764c9.1) \n- bd sync appeared to succeed\n- Canonical repo (~/src/beads): 162 issues in DB + JSONL ✓\n- Secondary repo (fred/beads): Only 145 issues vs 162 in canonical ✗\n- Both repos on same git commit but different issue counts!\n\n### Bug Manifestation During Recovery\n\n1. **Initial state**: fred/beads had 145 issues, 145 lines in JSONL, 145 export_hashes entries\n\n2. **After git reset --hard origin/main**: \n   - JSONL: 162 lines (from git)\n   - DB: 150 issues (auto-import partially worked)\n   - Auto-import failed with UNIQUE constraint error\n\n3. **After manual import --resolve-collisions**:\n   - DB: 160 issues\n   - JSONL: Still 162 lines\n   - export_hashes: 159 entries\n\n4. **After bd export**: \n   - **JSONL reduced to 17 lines!** ← The bug in action\n   - export_hashes: 159 entries (skipped exporting 142 issues)\n   - Silent data loss - no error message\n\n5. **After clearing export_hashes and re-export**:\n   - JSONL: 159 lines (missing 3 issues still)\n   - DB: 159 issues\n   - Still diverged from canonical\n\n### The Bug Loop\nOnce export_hashes and JSONL diverge:\n- Export skips issues already in export_hashes\n- But those issues aren't actually in JSONL\n- This creates corrupt JSONL with missing issues\n- Auto-import can't detect the problem (file hash matches what was exported)\n- Data is lost with no error messages\n\n### Recovery Solution\nCouldn't break the loop with export alone. Had to:\n1. Copy .beads/beads.db from canonical repo\n2. Clear export_hashes\n3. Full re-export\n4. Finally converged to 162 issues\n\n### Key Learnings\n\n1. **The bug is worse than we thought**: It can create corrupt exports (17 lines instead of 162!)\n\n2. **Auto-import can't save you**: Once export is corrupt, auto-import just imports the corrupt data\n\n3. **Silent failure**: No warnings, no errors, just missing issues\n\n4. **Git operations trigger it**: git reset, git pull, etc. change JSONL without clearing export_hashes\n\n5. **Import operations populate export_hashes**: Even manual imports update export_hashes, setting up future export failures\n\n### Immediate Action Required\n\n**DISABLE EXPORT DEDUPLICATION NOW**\n\nThis feature is fundamentally broken and causes data loss. Should be disabled until properly fixed.\n\nQuick fix options:\n- Set environment variable to disable feature\n- Comment out shouldSkipExport check\n- Always clear export_hashes before export\n- Add validation that DB count == JSONL line count before allowing export\n\n### Long-term Fix\n\nNeed Option 2 + 4 from proposed solutions:\n1. Store JSONL file hash after every successful export\n2. Before export, verify JSONL hash matches expected\n3. If mismatch, log WARNING and clear export_hashes\n4. Clear export_hashes on every import operation\n5. Add git post-merge hook to clear export_hashes\n6. Add `bd validate` command to detect divergence\n","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-10-29T23:05:13.959435-07:00","updated_at":"2025-10-30T17:12:58.207148-07:00","closed_at":"2025-10-29T21:57:03.06641-07:00"}
 {"id":"bd-5e1f","content_hash":"5b0aa7a2f651393bc13c46c172828acc4306d22d749ff71fbae96f0d25741847","title":"Issue with desc","description":"This is a description","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-10-31T21:41:11.128718-07:00","updated_at":"2025-11-02T16:40:27.356263-08:00","closed_at":"2025-11-02T16:40:27.356268-08:00"}
@@ -186,6 +186,7 @@
 {"id":"bd-be7a","content_hash":"d9043a7a49f8e42dc88c3c01aaa178c1560b67c1637c3373b39c387272e8b725","title":"Create npm package structure with package.json","description":"Set up initial npm package structure for @beads/bd:\n\n## Files to create\n- npm/package.json - Package metadata, dependencies, scripts\n- npm/bin/bd - CLI wrapper script that invokes native binary\n- npm/.gitignore - Ignore downloaded binaries\n- npm/README.md - Installation and usage instructions\n\n## package.json structure\n- Name: @beads/bd (scoped package)\n- Main: index.js (exports binary path)\n- Bin: bin/bd (CLI entry point)\n- Scripts: postinstall (download binary)\n- Keywords: issue-tracker, cli, beads, bd\n- License: MIT\n\n## Bin wrapper\nSimple Node.js script that:\n- Spawns native binary with child_process.spawn\n- Passes through all arguments and stdio\n- Exits with binary's exit code","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-02T23:39:47.416779-08:00","updated_at":"2025-11-03T10:31:45.381258-08:00","closed_at":"2025-11-03T10:31:45.381258-08:00","dependencies":[{"issue_id":"bd-be7a","depends_on_id":"bd-febc","type":"parent-child","created_at":"2025-11-02T23:40:32.923859-08:00","created_by":"daemon"}]}
 {"id":"bd-c01f","content_hash":"b183cc4d99f74e9314f67d927f1bd1255608632b47ce0352af97af5872275fec","title":"Implement bd stale command to find abandoned/forgotten issues","description":"Add bd stale command to surface issues that haven't been updated recently and may need attention.\n\nUse cases:\n- In-progress issues with no recent activity (may be abandoned)\n- Open issues that have been forgotten\n- Issues that might be outdated or no longer relevant\n\nQuery logic should find non-closed issues where updated_at exceeds a time threshold.\n\nShould support:\n- --days N flag (default 30-90 days)\n- --status filter (e.g., only in_progress)\n- --json output for automation\n\nReferences GitHub issue #184 where user expected this command to exist.","design":"Implementation approach:\n1. Add new command in cmd/bd/stale.go\n2. Query issues with: status != 'closed' AND updated_at \u003c (now - N days)\n3. Support filtering by status (open, in_progress, blocked)\n4. Default threshold: 30 days (configurable via --days)\n5. JSON output for agent consumption\n6. Order by updated_at ASC (oldest first)","status":"closed","priority":2,"issue_type":"epic","created_at":"2025-10-31T22:48:46.85435-07:00","updated_at":"2025-10-31T22:54:33.704492-07:00","closed_at":"2025-10-31T22:54:33.704492-07:00"}
 {"id":"bd-c362","content_hash":"3b9c44101d7f31fb6cbf4913873a4e140e74fbe7403907e8532bfaaabf875197","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 bd-e16b implementation.","status":"open","priority":3,"issue_type":"chore","created_at":"2025-11-02T18:34:02.831543-08:00","updated_at":"2025-11-02T18:34:02.831543-08:00","dependencies":[{"issue_id":"bd-c362","depends_on_id":"bd-e16b","type":"blocks","created_at":"2025-11-02T18:34:02.832607-08:00","created_by":"daemon"}]}
+{"id":"bd-c54b","content_hash":"a3d37caf244691a47e839fa78acc06ee88509a8347e7602a1d49385e3c2ea062","title":"SQLite driver creates database files with query params in filename","description":"The modernc.org/sqlite (or ncruces/go-sqlite3) driver is creating database files with the full connection string in the filename, including query parameters.\n\n**Current behavior:**\n`bd init` creates: `.beads/beads.db?_pragma=journal_mode(WAL)\u0026_pragma=foreign_keys(ON)\u0026_pragma=busy_timeout(30000)\u0026_time_format=sqlite`\n\n**Expected behavior:**\nShould create: `.beads/beads.db`\n\n**Root cause:**\nIn internal/storage/sqlite/sqlite.go:57, we append query params directly to the file path instead of using proper URI syntax with `file:` scheme.\n\n**Impact:**\n- Tests fail because they look for 'beads.db' but find the file with query params\n- Breaks gitignore patterns\n- Confusing for users\n- May cause issues with tools that parse .beads/ directory\n\n**Note on sqlite version:**\nWe're currently on an older version of the sqlite driver due to a previous database constraint error. We should investigate:\n1. Whether that constraint issue still happens with latest driver\n2. Whether upgrading would fix this filename issue\n3. Proper URI syntax for file paths with pragmas","status":"open","priority":0,"issue_type":"bug","created_at":"2025-11-03T15:05:09.113556-08:00","updated_at":"2025-11-03T15:05:09.113556-08:00"}
 {"id":"bd-c66a","content_hash":"60aebff5c08e0921b1c4285f4909da469c487fb7743658d3d292de8216013319","title":"Remove hardcoded issues.jsonl expectation - make JSONL filename configurable","description":"Currently bd expects the JSONL file to be named `issues.jsonl`, but this is hardcoded and breaks when users have `beads.jsonl` (the old/original filename).\n\nThe JSONL filename should be configurable via config.yaml, not hardcoded. This would allow:\n- Backward compatibility with existing beads.jsonl files\n- User choice of naming convention\n- Smoother migrations between versions\n\nContext: User has beads.jsonl and bd is failing to find it because it expects issues.jsonl.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-03T10:28:44.655972-08:00","updated_at":"2025-11-03T10:35:06.713125-08:00","closed_at":"2025-11-03T10:35:06.713125-08:00"}
 {"id":"bd-c77d","content_hash":"5d66618a9b287d1af262d989cb26932cb50b0cb0aa8e8e9365c3298a39db5f2d","title":"Test SQLite WASM compatibility","description":"Verify modernc.org/sqlite works in WASM target. Child of epic bd-44d0.\n\n## Tasks\n- [ ] Compile minimal SQLite test to WASM\n- [ ] Test database create/open operations\n- [ ] Test query execution\n- [ ] Test JSONL import/export\n- [ ] Benchmark performance vs native\n\n## Decision Point\nIf modernc.org/sqlite issues, evaluate ncruces/go-sqlite3 alternative.","status":"open","priority":0,"issue_type":"task","created_at":"2025-11-02T18:33:31.247537-08:00","updated_at":"2025-11-02T18:33:31.247537-08:00","dependencies":[{"issue_id":"bd-c77d","depends_on_id":"bd-197b","type":"blocks","created_at":"2025-11-02T18:33:31.248112-08:00","created_by":"daemon"}]}
 {"id":"bd-c796","content_hash":"3d36861edfa65fd43101c2ac0a2ec0a6bf931c84fcb2d6468a2e14f3fac367df","title":"Extract batch operations to batch_ops.go","description":"Move validateBatchIssues, generateBatchIDs, bulkInsertIssues, bulkRecordEvents, bulkMarkDirty, CreateIssues to batch_ops.go","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-01T19:28:54.887487-07:00","updated_at":"2025-11-01T23:38:31.841775-07:00","closed_at":"2025-11-01T23:38:31.841775-07:00"}
@@ -273,5 +274,3 @@
 {"id":"bd-fd56","content_hash":"71946aa48a3fa7836f905d340f73428416aeb8a190069ff3bb737eafbeed0d5e","title":"Wrap git operations in GitClient interface","description":"Create internal/daemonrunner/git.go with GitClient interface (HasUpstream, HasChanges, Commit, Push, Pull). Default implementation using os/exec. Use in Syncer and Run loop for testability.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-01T11:41:14.88734-07:00","updated_at":"2025-11-01T22:56:08.354697-07:00","closed_at":"2025-11-01T22:56:08.354697-07:00"}
 {"id":"bd-fd8753d9","content_hash":"ae13fc833baa7d586a48ca62648dd4f0ee61fcc96aa1f238fb2639b6657b07da","title":"Document bd edit command and verify MCP exclusion","description":"Follow-up from PR #152:\n1. Add \"bd edit\" to AGENTS.md with \"Humans only\" note\n2. Verify MCP server doesn't expose bd edit command\n3. Consider adding test for command registration","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-26T13:23:47.982295-07:00","updated_at":"2025-10-30T17:12:58.226229-07:00"}
 {"id":"bd-febc","content_hash":"686e0d5e3d56abe0edbd203d3d138ee3b013f55b6aed1eac05a56e6e3a5cc261","title":"npm package for bd with native binaries","description":"Create an npm package that wraps native bd binaries for easy installation in Claude Code for Web and other Node.js environments.\n\n## Problem\nClaude Code for Web sandboxes are full Linux VMs with npm support, but cannot easily download binaries from GitHub releases due to network restrictions or tooling limitations.\n\n## Solution\nPublish bd as an npm package that:\n- Downloads platform-specific native binaries during postinstall\n- Provides a CLI wrapper that invokes the native binary\n- Works seamlessly in Claude Code for Web SessionStart hooks\n- Maintains full feature parity (uses native SQLite)\n\n## Benefits vs WASM\n- ✅ Full SQLite support (no custom VFS needed)\n- ✅ All features work identically to native bd\n- ✅ Better performance (native vs WASM overhead)\n- ✅ ~4 hours effort vs ~2 days for WASM\n- ✅ Minimal maintenance burden\n\n## Success Criteria\n- npm install @beads/bd works in Claude Code for Web\n- All bd commands function identically to native binary\n- SessionStart hook documented for auto-installation\n- Package published to npm registry","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-11-02T23:39:37.684109-08:00","updated_at":"2025-11-03T10:39:44.932565-08:00","closed_at":"2025-11-03T10:39:44.932565-08:00"}
-{"id":"tst-4yrg","content_hash":"1da9cbeff48e405b1df7bfe8e750e27c0be0ff5fd253a81784d50597dd612219","title":"Test base36 ID in beads repo","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-03T11:19:52.273193-08:00","updated_at":"2025-11-03T11:19:52.273193-08:00"}
-{"id":"tst-6rni","content_hash":"8fcf8bd223896b510e50e48c172fde32162dd0fba238262eadca87a77f214a3c","title":"Testing base36 generation","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-03T11:19:46.194198-08:00","updated_at":"2025-11-03T11:19:46.194198-08:00"}
diff --git a/internal/storage/sqlite/sqlite.go b/internal/storage/sqlite/sqlite.go
index 10933f2c..1e155efc 100644
--- a/internal/storage/sqlite/sqlite.go
+++ b/internal/storage/sqlite/sqlite.go
@@ -49,13 +49,8 @@ func New(path string) (*SQLiteStorage, error) {
 	// _pragma=foreign_keys(ON) enforces foreign key constraints
 	// _pragma=busy_timeout(30000) means wait up to 30 seconds for locks instead of failing immediately
 	// _time_format=sqlite enables automatic parsing of DATETIME columns to time.Time
-	// Note: For shared memory URLs, additional params need to be added with & not ?
-	connStr := dbPath
-	if strings.Contains(dbPath, "?") {
-		connStr += "&_pragma=journal_mode(WAL)&_pragma=foreign_keys(ON)&_pragma=busy_timeout(30000)&_time_format=sqlite"
-	} else {
-		connStr += "?_pragma=journal_mode(WAL)&_pragma=foreign_keys(ON)&_pragma=busy_timeout(30000)&_time_format=sqlite"
-	}
+	// Use file: URI scheme to properly separate file path from query parameters
+	connStr := "file:" + dbPath + "?_pragma=journal_mode(WAL)&_pragma=foreign_keys(ON)&_pragma=busy_timeout(30000)&_time_format=sqlite"
 
 	db, err := sql.Open("sqlite3", connStr)
 	if err != nil {