Merge branch 'main' of github.com:steveyegge/beads

.beads/.gitignore

@@ -0,0 +1,24 @@
+# SQLite databases
+*.db
+*.db-journal
+*.db-wal
+*.db-shm
+
+# Daemon runtime files
+daemon.lock
+daemon.log
+daemon.pid
+bd.sock
+
+# Legacy database files
+db.sqlite
+bd.db
+
+# Keep JSONL exports and config (source of truth for git)
+!*.jsonl
+!metadata.json
+!config.json
+
+# Exclude merge artifacts (temporary files from 3-way merge)
+beads.base.jsonl
+beads.left.jsonl

cmd/bd/export.go

@@ -95,10 +95,18 @@ Output to stdout by default, or use -o flag for file output.`,
 			os.Exit(1)
 		}
 
-		// Export command doesn't work with daemon - need direct access
+		// Export command requires direct database access for consistent snapshot
+		// If daemon is connected, close it and open direct connection
+		if daemonClient != nil {
+			if os.Getenv("BD_DEBUG") != "" {
+				fmt.Fprintf(os.Stderr, "Debug: export command forcing direct mode (closes daemon connection)\n")
+			}
+			_ = daemonClient.Close()
+			daemonClient = nil
+		}
+		
 		// Ensure we have a direct store connection
 		if store == nil {
-			// Initialize store directly even if daemon is running
 			var err error
 			if dbPath == "" {
 				fmt.Fprintf(os.Stderr, "Error: no database path found\n")

cmd/bd/import.go

@@ -10,6 +10,7 @@ import (
 	"strings"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
@@ -25,8 +26,30 @@ Behavior:
   - New issues are created
   - Collisions (same ID, different content) are detected and reported
   - Use --dedupe-after to find and merge content duplicates after import
-  - Use --dry-run to preview changes without applying them`,
+  - Use --dry-run to preview changes without applying them
+
+NOTE: Import requires direct database access and does not work with daemon mode.
+      The command automatically uses --no-daemon when executed.`,
 	Run: func(cmd *cobra.Command, args []string) {
+		// Import requires direct database access due to complex transaction handling
+		// and collision detection. Force direct mode regardless of daemon state.
+		if daemonClient != nil {
+			if os.Getenv("BD_DEBUG") != "" {
+				fmt.Fprintf(os.Stderr, "Debug: import command forcing direct mode (closes daemon connection)\n")
+			}
+			_ = daemonClient.Close()
+			daemonClient = nil
+			
+			// Now initialize direct store
+			var err error
+			store, err = sqlite.New(dbPath)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error: failed to open database: %v\n", err)
+				os.Exit(1)
+			}
+			defer func() { _ = store.Close() }()
+		}
+
 		input, _ := cmd.Flags().GetString("input")
 		skipUpdate, _ := cmd.Flags().GetBool("skip-existing")
 		strict, _ := cmd.Flags().GetBool("strict")

cmd/bd/migrate_hash_ids.go

@@ -326,21 +326,29 @@ func replaceIDReferences(text string, mapping map[string]string) string {
 
 // isHashID checks if an ID is hash-based (not sequential)
 func isHashID(id string) bool {
-	// Hash IDs contain hex characters after the prefix
-	// Sequential IDs are only digits
+	// Hash IDs contain hex letters (a-f), sequential IDs are only digits
+	// May have hierarchical suffix like .1 or .1.2
 	parts := strings.SplitN(id, "-", 2)
 	if len(parts) != 2 {
 		return false
 	}
 	
-	// Check if the suffix starts with a hex digit (a-f)
 	suffix := parts[1]
-	if len(suffix) == 0 {
+	// Strip hierarchical suffix like .1 or .1.2
+	baseSuffix := strings.Split(suffix, ".")[0]
+	
+	if len(baseSuffix) == 0 {
 		return false
 	}
 	
-	// If it contains any letter a-f, it's a hash ID
-	return regexp.MustCompile(`[a-f]`).MatchString(suffix)
+	// Must be valid hex
+	if !regexp.MustCompile(`^[0-9a-f]+$`).MatchString(baseSuffix) {
+		return false
+	}
+	
+	// If it contains letters a-f, it's a hash ID
+	// Sequential IDs are only digits 0-9
+	return regexp.MustCompile(`[a-f]`).MatchString(baseSuffix)
 }
 
 // saveMappingFile saves the ID mapping to a JSON file

examples/git-hooks/README.md

@@ -1,21 +1,29 @@
 # bd Git Hooks
 
-This directory contains git hooks that integrate bd (beads) with your git workflow, solving the race condition between daemon auto-flush and git commits.
+This directory contains git hooks that integrate bd (beads) with your git workflow, preventing stale JSONL from being pushed to remote.
 
 ## The Problem
 
-When using bd in daemon mode, operations trigger a 5-second debounced auto-flush to JSONL. This creates a race condition:
+Two race conditions can occur:
 
-1. User closes issue via MCP → daemon schedules flush (5 sec delay)
-2. User commits code changes → JSONL appears clean
-3. Daemon flush fires → JSONL modified after commit
-4. Result: dirty working tree showing JSONL changes
+1. **Between operations and commits**: Daemon auto-flush (5s debounce) may fire after commit
+   - User closes issue via MCP → daemon schedules flush (5 sec delay)
+   - User commits code changes → JSONL appears clean
+   - Daemon flush fires → JSONL modified after commit
+   - Result: dirty working tree showing JSONL changes
+
+2. **Between commits and pushes**: Changes made after commit but before push (bd-my64)
+   - User commits → pre-commit hook flushes JSONL
+   - User adds comments or updates issues
+   - User pushes → outdated JSONL is pushed
+   - Result: remote has stale JSONL
 
 ## The Solution
 
-These git hooks ensure bd changes are always synchronized with your commits:
+These git hooks ensure bd changes are always synchronized with your commits and pushes:
 
-- **pre-commit** - Flushes pending bd changes to JSONL before commit
+- **pre-commit** - Flushes pending bd changes to JSONL before commit and stages it
+- **pre-push** - Blocks push if JSONL has uncommitted changes (bd-my64)
 - **post-merge** - Imports updated JSONL after git pull/merge
 
 ## Installation
@@ -37,8 +45,9 @@ This will:
 
 ```bash
 cp examples/git-hooks/pre-commit .git/hooks/pre-commit
+cp examples/git-hooks/pre-push .git/hooks/pre-push
 cp examples/git-hooks/post-merge .git/hooks/post-merge
-chmod +x .git/hooks/pre-commit .git/hooks/post-merge
+chmod +x .git/hooks/pre-commit .git/hooks/pre-push .git/hooks/post-merge
 ```
 
 ## How It Works
@@ -58,16 +67,33 @@ This:
 
 The hook is silent on success, fast (no git operations), and safe (fails commit if flush fails).
 
+### pre-push
+
+Before each push, the hook:
+
+```bash
+bd sync --flush-only  # Flush pending changes (if bd available)
+git status --porcelain .beads/*.jsonl  # Check for uncommitted changes
+```
+
+This prevents pushing stale JSONL by:
+1. Flushing pending in-memory changes from daemon's 5s debounce
+2. Checking for uncommitted changes (staged, unstaged, untracked, deleted)
+3. Failing the push with clear error message if changes exist
+4. Instructing user to commit JSONL before pushing again
+
+This solves bd-my64: changes made between commit and push (or pending debounced flushes) are caught before reaching remote.
+
 ### post-merge
 
 After a git pull or merge, the hook runs:
 
 ```bash
-bd import -i .beads/issues.jsonl
+bd import -i .beads/beads.jsonl
 ```
 
 This ensures your local database reflects the merged state. The hook:
-- Only runs if `.beads/issues.jsonl` exists
+- Only runs if `.beads/beads.jsonl` exists (also checks `issues.jsonl` for backward compat)
 - Imports any new issues or updates from the merge
 - Warns on failure but doesn't block the merge
 
@@ -92,7 +118,7 @@ This ensures your local database reflects the merged state. The hook:
 Remove the hooks:
 
 ```bash
-rm .git/hooks/pre-commit .git/hooks/post-merge
+rm .git/hooks/pre-commit .git/hooks/pre-push .git/hooks/post-merge
 ```
 
 Your backed-up hooks (if any) are in `.git/hooks/*.backup-*`.

examples/git-hooks/install.sh

@@ -59,7 +59,7 @@ echo "✓ Git hooks installed successfully"
 echo ""
 echo "Hooks installed:"
 echo "  pre-commit  - Flushes pending bd changes to JSONL before commit"
+echo "  pre-push    - Blocks push if JSONL has uncommitted changes (bd-my64)"
 echo "  post-merge  - Imports updated JSONL after git pull/merge"
-echo "  pre-push    - Exports database to JSONL before push (prevents stale JSONL)"
 echo ""
 echo "To uninstall, remove the hooks from .git/hooks/"

examples/git-hooks/pre-commit

@@ -4,7 +4,7 @@
 # bd (beads) pre-commit hook
 #
 # This hook ensures that any pending bd issue changes are flushed to
-# .beads/issues.jsonl before the commit is created, preventing the
+# .beads/beads.jsonl before the commit is created, preventing the
 # race condition where daemon auto-flush fires after the commit.
 #
 # Installation:
@@ -35,9 +35,10 @@ if ! bd sync --flush-only >/dev/null 2>&1; then
     exit 1
 fi
 
-# If the JSONL file was modified, stage it
-if [ -f .beads/issues.jsonl ]; then
-    git add .beads/issues.jsonl 2>/dev/null || true
-fi
+# Stage both possible JSONL files (backward compatibility)
+# git add is harmless if file doesn't exist
+for f in .beads/beads.jsonl .beads/issues.jsonl; do
+    [ -f "$f" ] && git add "$f" 2>/dev/null || true
+done
 
 exit 0

examples/git-hooks/pre-push

@@ -3,9 +3,14 @@
 #
 # bd (beads) pre-push hook
 #
-# This hook ensures that the database is exported to JSONL before pushing,
-# preventing the problem where database changes are committed without
-# corresponding JSONL updates.
+# This hook prevents pushing stale JSONL by:
+# 1. Flushing any pending in-memory changes to JSONL (if bd available)
+# 2. Checking for uncommitted changes (staged, unstaged, untracked, deleted)
+# 3. Failing the push with clear instructions if changes found
+#
+# The pre-commit hook already exports changes, but this catches:
+# - Changes made between commit and push
+# - Pending debounced flushes (5s daemon delay)
 #
 # Installation:
 #   cp examples/git-hooks/pre-push .git/hooks/pre-push
@@ -14,38 +19,43 @@
 # Or use the install script:
 #   examples/git-hooks/install.sh
 
-# Check if bd is available
-if ! command -v bd >/dev/null 2>&1; then
-    echo "Warning: bd command not found, skipping pre-push export check" >&2
-    exit 0
-fi
-
 # Check if we're in a bd workspace
 if [ ! -d .beads ]; then
     # Not a bd workspace, nothing to do
     exit 0
 fi
 
-# Check if database is newer than JSONL
-DB_FILE=".beads/beads.db"
-JSONL_FILE=".beads/beads.jsonl"
+# Optionally flush pending bd changes so they surface in JSONL
+# This prevents the race where a debounced flush lands after the check
+if command -v bd >/dev/null 2>&1; then
+    bd sync --flush-only >/dev/null 2>&1 || true
+fi
 
-if [ -f "$DB_FILE" ] && [ -f "$JSONL_FILE" ]; then
-    # Get modification times
-    if [ "$DB_FILE" -nt "$JSONL_FILE" ]; then
-        echo "⚠️  Database is newer than JSONL - exporting before push..." >&2
-        
-        # Force export to ensure JSONL is up to date
-        if ! BEADS_NO_DAEMON=1 bd export --output "$JSONL_FILE" >/dev/null 2>&1; then
-            echo "Error: Failed to export database to JSONL" >&2
-            echo "Run 'bd export' manually to diagnose" >&2
-            exit 1
-        fi
-        
-        # Stage the updated JSONL
-        git add "$JSONL_FILE" 2>/dev/null || true
-        
-        echo "✓ Exported database to JSONL" >&2
+# Collect all tracked or existing JSONL files (supports both old and new names)
+FILES=""
+for f in .beads/beads.jsonl .beads/issues.jsonl; do
+    # Include file if it exists in working tree OR is tracked by git (even if deleted)
+    if git ls-files --error-unmatch "$f" >/dev/null 2>&1 || [ -f "$f" ]; then
+        FILES="$FILES $f"
+    fi
+done
+
+# Check for any uncommitted changes using porcelain status
+# This catches: staged, unstaged, untracked, deleted, renamed, and conflicts
+if [ -n "$FILES" ]; then
+    # shellcheck disable=SC2086
+    if [ -n "$(git status --porcelain -- $FILES 2>/dev/null)" ]; then
+        echo "❌ Error: Beads JSONL has uncommitted changes" >&2
+        echo "" >&2
+        echo "You made changes to bd issues between your last commit and this push." >&2
+        echo "Please commit the updated JSONL before pushing:" >&2
+        echo "" >&2
+        # shellcheck disable=SC2086
+        echo "  git add $FILES" >&2
+        echo '  git commit -m "Update bd JSONL"' >&2
+        echo "  git push" >&2
+        echo "" >&2
+        exit 1
     fi
 fi